[gmx-users] How to combine Slipid FF with amber FF?

Discussion:

Yorquant Wang

2014-08-31 10:59:11 UTC

Hi all,
I want to do a membrane protein simulation and I want to use amber FF
for protein (my target protein contains many beta sheet secondary
structures). But forcefield.ff file in the web:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
lipids parameter. I don't know how to conbined those lipid parameter
with amber99sb-ildn.ff.
Is there anybody who can help me? Thank you very much.

--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

rajat desikan

2014-08-31 12:20:47 UTC

Permalink

Hi,

Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber FF).

; Include lipid topology
#include "./DMPC.itp"

Of course, you can change the name of the lipid.itp according to the
lipids in your system.

The order in which this appears in your .top matters. If you add the
lipids to your simulation box and then solvate it, the above line must
come prior to the water.itp

Regards,

Post by Yorquant Wang
Hi all,
I want to do a membrane protein simulation and I want to use amber FF
for protein (my target protein contains many beta sheet secondary
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
lipids parameter. I don't know how to conbined those lipid parameter
with amber99sb-ildn.ff.
Is there anybody who can help me? Thank you very much.
--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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mail to gmx-users-request at gromacs.org.

--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

Yorquant Wang

2014-08-31 12:42:53 UTC

Permalink

Hi,
I have done that according to your advice and when I do the command
grompp, I get such a error:
Fatal error:
Atomtype NTL not found
---------------------
this is my top file:

#include "amber99sb-ildn.ff/forcefield.itp"
#include "POPC.itp"
#include "protein-amber.itp"
#include "amber99sb-ildn.ff/ions.itp"
#include "amber99sb-ildn.ff/tip3p.itp"

[ system ]
; Name
membrane protein
[ molecules ]
; Compound #mols

protein 2
POPC 72
SOL 3337
NA 18
CL 22

Post by rajat desikan
Hi,
Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber FF).
; Include lipid topology
#include "./DMPC.itp"
Of course, you can change the name of the lipid.itp according to the
lipids in your system.
The order in which this appears in your .top matters. If you add the
lipids to your simulation box and then solvate it, the above line must
come prior to the water.itp
Regards,

Post by Yorquant Wang
Hi all,
I want to do a membrane protein simulation and I want to use amber

Post by Yorquant Wang
for protein (my target protein contains many beta sheet secondary
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
lipids parameter. I don't know how to conbined those lipid parameter
with amber99sb-ildn.ff.
Is there anybody who can help me? Thank you very much.
--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

posting!

Post by Yorquant Wang
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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send a

Post by Yorquant Wang
mail to gmx-users-request at gromacs.org.

--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
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send a mail to gmx-users-request at gromacs.org.

--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

Justin Lemkul

2014-08-31 13:06:45 UTC

Permalink

Post by Yorquant Wang
Hi,
I have done that according to your advice and when I do the command
Atomtype NTL not found
---------------------
#include "amber99sb-ildn.ff/forcefield.itp"
#include "POPC.itp"
#include "protein-amber.itp"
#include "amber99sb-ildn.ff/ions.itp"
#include "amber99sb-ildn.ff/tip3p.itp"

You get the error because none of these files knows anything about Slipids
parameters except POPC.itp, which tries to use them. So grompp fails. See my
previous reply; you need to modify the force field.

-Justin

Post by Yorquant Wang
[ system ]
; Name
membrane protein
[ molecules ]
; Compound #mols
protein 2
POPC 72
SOL 3337
NA 18
CL 22

Post by Yorquant Wang
Hi all,
I want to do a membrane protein simulation and I want to use amber

posting!

Post by Yorquant Wang
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

send a

Post by Yorquant Wang
mail to gmx-users-request at gromacs.org.

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

rajat desikan

2014-08-31 13:13:34 UTC

Permalink

Hi,
I assumed that you had gone through the forcefield.ff files on Slipids
webpage. You need to include the following section at the end in your
ffnonbonded.itp (some of the spaces may be missing below). I suggest
modifying a local copy of your desired Amber ff.

; SLIPIDS STARTS HERE
HAL1 1 1.008000 0.09 A 0.235197261589 0.092048
HL 1 1.008000 0.25 A 0.12472582054 0.192464
HEL1 1 1.008000 0.15 A 0.2 0.10 ; New
CL 6 12.01100 0.62 A 0.356359487256 0.29288
CTL1 6 12.01100 0.14 A 0.405358916754 0.08368
CTL3 6 12.0111 -0.081 A 0.35000 0.3400 ; New
CTL2 6 12.0011 0.05 A 0.35800 0.22800 ; New
HAL3 1 1.00800 0.09 A 0.22000 0.09500 ; New
HAL2 1 1.00800 0.09 A 0.24000 0.1120 ; New
CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
CEL1 6 12.01100 -0.15 A 0.35 0.22 ; New
CET1 6 12.01100 -0.15 A 0.35 0.22 ; New, for trans double-bond
OBL 8 15.999400 -0.52 A 0.302905564168 0.50208
OCL 8 15.999400 -0.76 A 0.302905564168 0.50208
O2L 8 15.999400 -0.78 A 0.302905564168 0.50208
OSL 8 15.999400 -0.49 A 0.293996576986 0.4184 ; Different to C27
OSLP 8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27
NTL 7 14.00700 -0.60 A 0.329632525712 0.8368
PL 15 30.974000 1.50 A 0.3830864488 2.44764
HOL 1 1.008000 0.43 A 0.0400013524445 0.192464
OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864
NH3L 7 14.00700 -0.30 A 0.329632525712 0.8368
HCL 1 1.008000 0.33 A 0.0400013524445 0.192464
CCL 6 12.01100 0.34 A 0.356359487256 0.29288
HBL 1 1.008000 0.10 A 0.235197261589 0.092048
NH1 7 14.00700 -0.47 A 0.329632525712 0.8368
H11 1 1.008000 0.31 A 0.0400013524445 0.192464

[ pairtypes ]
; 1-4 interactions
; i j func sigma1-4 epsilon1-4
CTL1 CTL1 1 0.338541512893 0.04184
CTL1 CTL2 1 0.338541512893 0.04184
CTL1 CTL3 1 0.338541512893 0.04184
CTL1 CTL5 1 0.338541512893 0.04184
CTL1 OBL 1 0.293996576986 0.144938011577
CTL1 HAL1 1 0.286869387241 0.06205874894
CTL1 HAL2 1 0.288651184678 0.0700117110204
CTL1 HAL3 1 0.288651184678 0.0648182492821
CTL1 HL 1 0.231633666716 0.0897368027066
CTL1 HEL1 1 0.280633096214 0.0736669217492
CTL1 CEL1 1 0.355468588538 0.109105371453
CTL1 CET1 1 0.355468588538 0.109105371453
CTL1 OSL 1 0.316269044940 0.132309697301
CTL1 OSLP 1 0.316269044940 0.132309697301
CTL1 NTL 1 0.334087019303 0.187114168357
CTL1 PL 1 0.360813980846 0.320014464673
CTL1 HOL 1 0.189271432669 0.0897368027066
CTL1 OHL 1 0.326959829558 0.163176
;
CTL2 CTL2 1 0.321 0.08184 ; New
CTL2 HAL2 1 0.268651184678 0.0200117110204 ; New
CTL2 CTL3 1 0.325 0.10184 ; New
CTL3 HAL2 1 0.278651184678 0.0200117110204 ; New
CTL2 CTL5 1 0.338541512893 0.04184
CTL2 OBL 1 0.293996576986 0.144938011577
CTL2 HAL1 1 0.286869387241 0.06205874894
CTL2 HAL3 1 0.288651184678 0.0648182492821
CTL2 HL 1 0.231633666716 0.0897368027066
CTL2 HEL1 1 0.280633096214 0.0736669217492
CTL2 CL 1 0.347450500074 0.110698234855
CTL2 CEL1 1 0.355468588538 0.109105371453
CTL2 CET1 1 0.355468588538 0.109105371453
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 O2L 1 0.320723538531 0.144938011577
CTL2 OSL 1 0.316269044940 0.132309697301
CTL2 OSLP 1 0.316269044940 0.132309697301
CTL2 NTL 1 0.334087019303 0.187114168357
CTL2 PL 1 0.360813980846 0.320014464673
CTL2 HOL 1 0.189271432669 0.0897368027066
CTL2 OHL 1 0.326959829558 0.163176
CTL2 HCL 1 0.189271432669 0.0897368027066
CTL2 NH3L 1 0.334087019303 0.187114168357
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 HCL 1 0.189271432669 0.0897368027066
;
CTL3 CTL3 1 0.338541512893 0.04184
CTL3 CTL5 1 0.338541512893 0.04184
CTL3 OBL 1 0.293996576986 0.144938011577
CTL3 HL 1 0.231633666716 0.0897368027066
CTL3 HEL1 1 0.280633096214 0.0736669217492
CTL3 CL 1 0.347450500074 0.110698234855
CTL3 CEL1 1 0.355468588538 0.109105371453
CTL3 CET1 1 0.355468588538 0.109105371453
CTL3 O2L 1 0.320723538531 0.144938011577
CTL3 OSL 1 0.316269044940 0.132309697301
CTL3 OSLP 1 0.316269044940 0.132309697301
CTL3 NTL 1 0.334087019303 0.187114168357
CTL3 PL 1 0.360813980846 0.320014464673
CTL3 HOL 1 0.189271432669 0.0897368027066
CTL3 OHL 1 0.326959829558 0.163176
;
CTL5 CTL5 1 0.338541512893 0.04184
CTL5 OBL 1 0.293996576986 0.144938011577
CTL5 HAL1 1 0.286869387241 0.06205874894
CTL5 HAL2 1 0.288651184678 0.0700117110204
CTL5 HAL3 1 0.288651184678 0.0648182492821
CTL5 HL 1 0.231633666716 0.0897368027066
CTL5 HEL1 1 0.280633096214 0.0736669217492
CTL5 CL 1 0.347450500074 0.110698234855
CTL5 CEL1 1 0.355468588538 0.109105371453
CTL5 CET1 1 0.355468588538 0.109105371453
CTL5 OCL 1 0.320723538531 0.144938011577
CTL5 O2L 1 0.320723538531 0.144938011577
CTL5 OSL 1 0.316269044940 0.132309697301
CTL5 OSLP 1 0.316269044940 0.132309697301
CTL5 NTL 1 0.334087019303 0.187114168357
CTL5 PL 1 0.360813980846 0.320014464673
;
OBL OBL 1 0.249451641079 0.50208
OBL HAL1 1 0.242324451334 0.214977812437
OBL HAL2 1 0.24410624877 0.242527681224
OBL HAL3 1 0.24410624877 0.224537002029
OBL HL 1 0.18708873081 0.310857403193
OBL HEL1 1 0.236088160307 0.255189702614
OBL CL 1 0.302905564167 0.383469934154
OBL CEL1 1 0.310923652631 0.377952093472
OBL CET1 1 0.310923652631 0.377952093472
OBL OCL 1 0.276178602624 0.50208
OBL O2L 1 0.276178602624 0.50208
OBL OSL 1 0.271724109033 0.45833423612
OBL OSLP 1 0.271724109033 0.45833423612
OBL NTL 1 0.289542083396 0.648182492821
OBL PL 1 0.316269044939 1.10856262394

Similarly, you have to make changes in the ffbonded.itp as well (add
bond, angle, proper and improper dihedral definitions). Go through the
Slipid forcefield.ff files carefully.

Yorquant Wang

2014-09-01 13:55:41 UTC

Permalink

Hi,
Thank you for your reply. I have added the parameters from Slipid to
amber FF files (including: atomtypes.atp, ffbonded.itp, ffnonbonded.itp). I
also get such an error.
ERROR 1 [file ffbonded.itp, line 410]:
Not enough atomtypes (1 instead of 3)

I just patch two atomtypes.atp (one from amber and another one from Slipid)
together. Could you give me some seggestions? thanks !

Post by rajat desikan
Hi,
I assumed that you had gone through the forcefield.ff files on Slipids
webpage. You need to include the following section at the end in your
ffnonbonded.itp (some of the spaces may be missing below). I suggest
modifying a local copy of your desired Amber ff.
; SLIPIDS STARTS HERE
HAL1 1 1.008000 0.09 A 0.235197261589 0.092048
HL 1 1.008000 0.25 A 0.12472582054 0.192464
HEL1 1 1.008000 0.15 A 0.2 0.10
; New
CL 6 12.01100 0.62 A 0.356359487256 0.29288
CTL1 6 12.01100 0.14 A 0.405358916754 0.08368
CTL3 6 12.0111 -0.081 A 0.35000 0.3400
; New
CTL2 6 12.0011 0.05 A 0.35800 0.22800
; New
HAL3 1 1.00800 0.09 A 0.22000 0.09500
; New
HAL2 1 1.00800 0.09 A 0.24000 0.1120
; New
CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
CEL1 6 12.01100 -0.15 A 0.35 0.22
; New
CET1 6 12.01100 -0.15 A 0.35 0.22
; New, for trans double-bond
OBL 8 15.999400 -0.52 A 0.302905564168 0.50208
OCL 8 15.999400 -0.76 A 0.302905564168 0.50208
O2L 8 15.999400 -0.78 A 0.302905564168 0.50208
OSL 8 15.999400 -0.49 A 0.293996576986 0.4184
; Different to C27
OSLP 8 15.999400 -0.57 A 0.293996576986 0.4184
; Not in C27
NTL 7 14.00700 -0.60 A 0.329632525712 0.8368
PL 15 30.974000 1.50 A 0.3830864488 2.44764
HOL 1 1.008000 0.43 A 0.0400013524445 0.192464
OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864
NH3L 7 14.00700 -0.30 A 0.329632525712 0.8368
HCL 1 1.008000 0.33 A 0.0400013524445 0.192464
CCL 6 12.01100 0.34 A 0.356359487256 0.29288
HBL 1 1.008000 0.10 A 0.235197261589 0.092048
NH1 7 14.00700 -0.47 A 0.329632525712 0.8368
H11 1 1.008000 0.31 A 0.0400013524445 0.192464
[ pairtypes ]
; 1-4 interactions
; i j func sigma1-4 epsilon1-4
CTL1 CTL1 1 0.338541512893 0.04184
CTL1 CTL2 1 0.338541512893 0.04184
CTL1 CTL3 1 0.338541512893 0.04184
CTL1 CTL5 1 0.338541512893 0.04184
CTL1 OBL 1 0.293996576986 0.144938011577
CTL1 HAL1 1 0.286869387241 0.06205874894
CTL1 HAL2 1 0.288651184678 0.0700117110204
CTL1 HAL3 1 0.288651184678 0.0648182492821
CTL1 HL 1 0.231633666716 0.0897368027066
CTL1 HEL1 1 0.280633096214 0.0736669217492
CTL1 CEL1 1 0.355468588538 0.109105371453
CTL1 CET1 1 0.355468588538 0.109105371453
CTL1 OSL 1 0.316269044940 0.132309697301
CTL1 OSLP 1 0.316269044940 0.132309697301
CTL1 NTL 1 0.334087019303 0.187114168357
CTL1 PL 1 0.360813980846 0.320014464673
CTL1 HOL 1 0.189271432669 0.0897368027066
CTL1 OHL 1 0.326959829558 0.163176
;
CTL2 CTL2 1 0.321 0.08184 ; New
CTL2 HAL2 1 0.268651184678 0.0200117110204 ; New
CTL2 CTL3 1 0.325 0.10184 ; New
CTL3 HAL2 1 0.278651184678 0.0200117110204 ; New
CTL2 CTL5 1 0.338541512893 0.04184
CTL2 OBL 1 0.293996576986 0.144938011577
CTL2 HAL1 1 0.286869387241 0.06205874894
CTL2 HAL3 1 0.288651184678 0.0648182492821
CTL2 HL 1 0.231633666716 0.0897368027066
CTL2 HEL1 1 0.280633096214 0.0736669217492
CTL2 CL 1 0.347450500074 0.110698234855
CTL2 CEL1 1 0.355468588538 0.109105371453
CTL2 CET1 1 0.355468588538 0.109105371453
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 O2L 1 0.320723538531 0.144938011577
CTL2 OSL 1 0.316269044940 0.132309697301
CTL2 OSLP 1 0.316269044940 0.132309697301
CTL2 NTL 1 0.334087019303 0.187114168357
CTL2 PL 1 0.360813980846 0.320014464673
CTL2 HOL 1 0.189271432669 0.0897368027066
CTL2 OHL 1 0.326959829558 0.163176
CTL2 HCL 1 0.189271432669 0.0897368027066
CTL2 NH3L 1 0.334087019303 0.187114168357
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 HCL 1 0.189271432669 0.0897368027066
;
CTL3 CTL3 1 0.338541512893 0.04184
CTL3 CTL5 1 0.338541512893 0.04184
CTL3 OBL 1 0.293996576986 0.144938011577
CTL3 HL 1 0.231633666716 0.0897368027066
CTL3 HEL1 1 0.280633096214 0.0736669217492
CTL3 CL 1 0.347450500074 0.110698234855
CTL3 CEL1 1 0.355468588538 0.109105371453
CTL3 CET1 1 0.355468588538 0.109105371453
CTL3 O2L 1 0.320723538531 0.144938011577
CTL3 OSL 1 0.316269044940 0.132309697301
CTL3 OSLP 1 0.316269044940 0.132309697301
CTL3 NTL 1 0.334087019303 0.187114168357
CTL3 PL 1 0.360813980846 0.320014464673
CTL3 HOL 1 0.189271432669 0.0897368027066
CTL3 OHL 1 0.326959829558 0.163176
;
CTL5 CTL5 1 0.338541512893 0.04184
CTL5 OBL 1 0.293996576986 0.144938011577
CTL5 HAL1 1 0.286869387241 0.06205874894
CTL5 HAL2 1 0.288651184678 0.0700117110204
CTL5 HAL3 1 0.288651184678 0.0648182492821
CTL5 HL 1 0.231633666716 0.0897368027066
CTL5 HEL1 1 0.280633096214 0.0736669217492
CTL5 CL 1 0.347450500074 0.110698234855
CTL5 CEL1 1 0.355468588538 0.109105371453
CTL5 CET1 1 0.355468588538 0.109105371453
CTL5 OCL 1 0.320723538531 0.144938011577
CTL5 O2L 1 0.320723538531 0.144938011577
CTL5 OSL 1 0.316269044940 0.132309697301
CTL5 OSLP 1 0.316269044940 0.132309697301
CTL5 NTL 1 0.334087019303 0.187114168357
CTL5 PL 1 0.360813980846 0.320014464673
;
OBL OBL 1 0.249451641079 0.50208
OBL HAL1 1 0.242324451334 0.214977812437
OBL HAL2 1 0.24410624877 0.242527681224
OBL HAL3 1 0.24410624877 0.224537002029
OBL HL 1 0.18708873081 0.310857403193
OBL HEL1 1 0.236088160307 0.255189702614
OBL CL 1 0.302905564167 0.383469934154
OBL CEL1 1 0.310923652631 0.377952093472
OBL CET1 1 0.310923652631 0.377952093472
OBL OCL 1 0.276178602624 0.50208
OBL O2L 1 0.276178602624 0.50208
OBL OSL 1 0.271724109033 0.45833423612
OBL OSLP 1 0.271724109033 0.45833423612
OBL NTL 1 0.289542083396 0.648182492821
OBL PL 1 0.316269044939 1.10856262394
Similarly, you have to make changes in the ffbonded.itp as well (add
bond, angle, proper and improper dihedral definitions). Go through the
Slipid forcefield.ff files carefully.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-request at gromacs.org.

--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

Justin Lemkul

2014-09-01 17:24:55 UTC

Permalink

Post by Yorquant Wang
Hi,
Thank you for your reply. I have added the parameters from Slipid to
amber FF files (including: atomtypes.atp, ffbonded.itp, ffnonbonded.itp). I
also get such an error.
Not enough atomtypes (1 instead of 3)
I just patch two atomtypes.atp (one from amber and another one from Slipid)
together. Could you give me some seggestions? thanks !

The error has nothing to do with atomtypes.atp, it's coming from ffbonded.itp
(line 410). It looks like you're adding a directive incorrectly. Atom type
parameters go in ffnonbonded.itp; the line above indicates that grompp is
looking for 3 atom types in sequence, so it wants an angle, but finds 1 atom type.

-Justin

Post by Yorquant Wang

Justin Lemkul

2014-08-31 13:05:57 UTC

Permalink

This is not true. The only case where #include statement order matters is if
new parameters are introduced. For any other simply .itp files that #include a
new [moleculetype], order is irrelevant. Order of appearance in [molecules]
must, however, match the order of appearance in the coordinate file.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

Justin Lemkul

2014-08-31 13:04:57 UTC

Permalink

You just need to combine the contents of ffbonded.itp and ffnonbonded.itp to
those same files in the parent protein force field. Copy and paste into the
relevant directives or (possibly, never tried it this way) rename the
ffbonded.itp and ffnonbonded.itp files from Slipids and simply #include them in
your .top after the #include statement for the force field. Not sure if that
will work, especially if new atom types are added.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================