Discussion:
[gmx-users] (no subject)
maya nair
2018-11-23 05:58:54 UTC
Permalink
I am trying to do the molecular dynamics of DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp ions.mdp and em.mdp, it gives error saying the following

Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
Too few gb parameters for type 1


Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.
Help me in this regard. I am attaching my files.
Thank you
Maya

[image: Attachments]
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
Justin Lemkul
2018-11-26 14:53:33 UTC
Permalink
Post by maya nair
I am trying to do the molecular dynamics of DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp ions.mdp and em.mdp, it gives error saying the following
gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772
Too few gb parameters for type 1
Couldn't find topology match for atomtype 1
Aborted (core dumped)
I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.
The .atp file is only read by pdb2gmx, so it's not relevant. Apparently
you have an atom type "1" (number one) in your topology, which is very
strange. It doesn't have parameters defined in gb.itp, so you get a
failure. Make sure your input is sound and your topology/force field
files are free of typos.
Post by maya nair
Help me in this regard. I am attaching my files.
This mailing list does not accept attachments. If you need to share
files, use a file-sharing service and provide the URL.

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
--
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-***@gromacs.org.
Soham Sarkar
2018-12-01 13:11:06 UTC
Permalink
Dear all,
This is the error I get while executing the grompp command
" Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
<https://www.researchgate.net/deref/http%3A%2F%2Fsystem.top> "
I am attaching the input files. I have generated the tris.itp from tppmktop
Justin Lemkul
2018-12-02 16:35:11 UTC
Permalink
Post by Soham Sarkar
Dear all,
This is the error I get while executing the grompp command
" Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Syntax error - File tris.itp, line 19
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
<https://www.researchgate.net/deref/http%3A%2F%2Fsystem.top> "
I am attaching the input files. I have generated the tris.itp from tppmktop
Attachments are not allowed on the mailing list.

There are several things to consider. The first is that version 4.5.6 is
ancient and no longer supported. Use a modern GROMACS version. The
second is to look at what is in the topology on line 19 to see how not
to trigger the error that you're getting.

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
--
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-***@gromacs.org.
Soham Sarkar
2018-12-02 16:42:45 UTC
Permalink
Dear all,
This is the error I get while executing the grompp command
" Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
<https://www.researchgate.net/deref/http%3A%2F%2Fsystem.top> "
I am attaching the input files. I have generated the tris.itp from tppmktop
maya nair
2018-12-03 11:02:33 UTC
Permalink
ERROR 1 [file res.itp, line 57]:
Invalid Atomnr j: 4, b2->nr: 3

I am getting the above error for the command

gmx grompp -f em.mdp -c solv.gro -p topol1.top -o ions.tpr. My res.itp file
is given below. I couldnot understand the meaning of this error. Can you
please help me? part of the .itp is appended here.


1.

trial_GMX.top created by acpype (Rev: 0) on Wed Nov 21 15:15:35 2018
2.
3.
4.

; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
5.

1 2 yes 0.5 0.8333
6.
7.

# include "ffnonbonded.itp"
8.

# include "ffbonded.itp"
9.

# include "gbsa.itp"
10.
11.
12.

;name bond_type mass charge ptype sigma epsilon Amb
13.

CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
14.

oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
15.

ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
16.

ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
17.

ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
18.

cf cf 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
19.
20.
21.

;name nrexcl
22.

STL 3
23.
24.

; nr type resi res atom cgnr charge mass ; qtot bond_type
25.

1 CA 1 STL C1 1 0.156600 12.01000 ; qtot 0.157
26.

2 oh 1 STL O1 2 -0.494100 16.00000 ; qtot -0.338
27.

3 ho 1 STL H1 3 0.420000 1.00800 ; qtot 0.083
28.

4 CA 1 STL C2 4 -0.185000 12.01000 ; qtot -0.103
29.

5 ha 1 STL H2 5 0.168000 1.00800 ; qtot 0.066
30.

6 oh 1 STL O2 6 -0.494100 16.00000 ; qtot -0.429
31.

7 ho 1 STL H5 7 0.420500 1.00800 ; qtot -0.008
32.

8 CA 1 STL C3 8 0.156600 12.01000 ; qtot 0.149
33.

9 oh 1 STL O3 9 -0.494100 16.00000 ; qtot -0.346
34.

10 ho 1 STL H3 10 0.420500 1.00800 ; qtot 0.075
35.

11 CA 1 STL C4 11 -0.240000 12.01000 ; qtot -0.165
36.

12 ha 1 STL H4 12 0.137000 1.00800 ; qtot -0.028
37.

13 CA 1 STL C5 13 0.023200 12.01000 ; qtot -0.005
38.

14 CA 1 STL C6 14 -0.240000 12.01000 ; qtot -0.245
39.

15 ha 1 STL H6 15 0.137000 1.00800 ; qtot -0.108
40.

16 ce 1 STL C7 16 -0.121200 12.01000 ; qtot -0.229
41.

17 ha 1 STL H7 17 0.130000 1.00800 ; qtot -0.099
42.

18 cf 1 STL C8 18 -0.085200 12.01000 ; qtot -0.184
43.

19 ha 1 STL H8 19 0.126000 1.00800 ; qtot -0.058
44.

20 CA 1 STL C9 20 -0.098800 12.01000 ; qtot -0.157
45.

21 CA 1 STL C10 21 -0.079500 12.01000 ; qtot -0.237
46.

22 ha 1 STL H10 22 0.136000 1.00800 ; qtot -0.101
47.

23 CA 1 STL C11 23 -0.187000 12.01000 ; qtot -0.288
48.

24 ha 1 STL H11 24 0.143500 1.00800 ; qtot -0.144
49.

25 CA 1 STL C12 25 0.131100 12.01000 ; qtot -0.013
50.

26 CA 1 STL C13 26 -0.187000 12.01000 ; qtot -0.200
51.

27 ha 1 STL H13 27 0.143500 1.00800 ; qtot -0.057
52.

28 CA 1 STL C14 28 -0.079500 12.01000 ; qtot -0.136
53.

29 ha 1 STL H14 29 0.136000 1.00800 ; qtot 0.000
54.
55.
56.

; ai aj funct r k
57.

1 4 1 1.3984e-01 3.8585e+05 ; C1 - C2
58.

1 9 1 1.3637e-01 3.2133e+05 ; C1 - O3
59.

1 14 1 1.3984e-01 3.8585e+05 ; C1 - C6
60.

2 3 1 9.7300e-02 3.1079e+05 ; O1 - H1
61.

2 25 1 1.3637e-01 3.2133e+05 ; O1 - C12
62.

4 5 1 1.0860e-01 2.8937e+05 ; C2 - H2
63.

4 8 1 1.3984e-01 3.8585e+05 ; C2 - C3
64.

6 7 1 9.7300e-02 3.1079e+05 ; O2 - H5
65.

6 8 1 1.3637e-01 3.2133e+05 ; O2 - C3
66.

8 11 1 1.3984e-01 3.8585e+05 ; C3 - C4
67.

9 10 1 9.7300e-02 3.1079e+05 ; O3 - H3
68.

11 12 1 1.0860e-01 2.8937e+05 ; C4 - H4
69.

11 13 1 1.3984e-01 3.8585e+05 ; C4 - C5
70.

13 14 1 1.3984e-01 3.8585e+05 ; C5 - C6
71.

13 16 1 1.4763e-01 3.0234e+05 ; C5 - C7
72.

14 15 1 1.0860e-01 2.8937e+05 ; C6 - H6
73.

16 17 1 1.0883e-01 2.8660e+05 ; C7 - H7
74.

16 18 1 1.3509e-01 4.5070e+05 ; C7 - C8
75.

18 19 1 1.0883e-01 2.8660e+05 ; C8 - H8
76.

18 20 1 1.4763e-01 3.0234e+05 ; C8 - C9
77.

20 21 1 1.3984e-01 3.8585e+05 ; C9 - C10
78.

20 28 1 1.3984e-01 3.8585e+05 ; C9 - C14
79.

21 22 1 1.0860e-01 2.8937e+05 ; C10 - H10
80.

21 23 1 1.3984e-01 3.8585e+05 ; C10 - C11
81.

23 24 1 1.0860e-01 2.8937e+05 ; C11 - H11
82.

23 25 1 1.3984e-01 3.8585e+05 ; C11 - C12
83.

25 26 1 1.3984e-01 3.8585e+05 ; C12 - C13
84.

26 27 1 1.0860e-01 2.8937e+05 ; C13 - H13
85.

26 28 1 1.3984e-01 3.8585e+05 ; C13 - C14
86.

28 29 1 1.0860e-01 2.8937e+05 ; C14 - H14
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
--
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-***@gromacs.org.
Continue reading on narkive:
Loading...