[gmx-users] Introducing DUMMY atom and top file modification

[Golshan Hejazi]

Hi everyone,

I wanna perform a TI using gromacs. For that I am modifying the top file in order to introduce dummy atoms and I am using charmm ff. I have already introduced a new molecule named PAR and I want to have another molecule in my simulation which is the PAR molecule turned to a DUMMY molecule.
In the top file, I have these lines for atom section:

[ atoms ]
; ? nr ? ? ? type ?resnr residue ?atom ? cgnr ? ? charge ? ? ? mass ?typeB ? ?chargeB ? ? ?massB
; residue ? 617 PAR rtp PAR ?q ?0.0
?12321 ? ? ?CG331 ? ?617 ? ?PAR ? ?CQ8 ?12321 ? ? ?-0.27 ? ? 12.011 ? ; qtot -0.27
?12322 ? ? ? HGA3 ? ?617 ? ?PAR ? ?HQ7 ?12322 ? ? ? 0.09 ? ? ?1.008 ? ; qtot -0.18
?12323 ? ? ? HGA3 ? ?617 ? ?PAR ? ?HQ8 ?12323 ? ? ? 0.09 ? ? ?1.008 ? ; qtot -0.09
?12324 ? ? ? HGA3 ? ?617 ? ?PAR ? ?HQ9 ?12324 ? ? ? 0.09 ? ? ?1.008 ? ; qtot 0
?12325 ? ? ?CG2O1 ? ?617 ? ?PAR ? ?CQ7 ?12325 ? ? ? 0.52 ? ? 12.011 ? ; qtot 0.52
?12326 ? ? ?OG2D1 ? ?617 ? ?PAR ? ?OQ2 ?12326 ? ? ?-0.52 ? ?15.9994 ? ; qtot 0
?12327 ? ? ?NG2S1 ? ?617 ? ?PAR ? ?NQ1 ?12327 ? ? ?-0.47 ? ? 14.007 ? ; qtot -0.47
?12328 ? ? ? HGP1 ? ?617 ? ?PAR ? ?HQ6 ?12328 ? ? ? 0.33 ? ? ?1.008 ? ; qtot -0.14
?12329 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ1 ?12329 ? ? ? 0.14 ? ? 12.011 ? ; qtot 0
?12330 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ6 ?12330 ? ? -0.115 ? ? 12.011 ? ; qtot -0.115
?12331 ? ? ?HGR61 ? ?617 ? ?PAR ? ?HQ5 ?12331 ? ? ?0.115 ? ? ?1.008 ? ; qtot 0
?12332 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ5 ?12332 ? ? -0.115 ? ? 12.011 ? ; qtot -0.115
?12333 ? ? ?HGR61 ? ?617 ? ?PAR ? ?HQ4 ?12333 ? ? ?0.115 ? ? ?1.008 ? ; qtot 0
?12334 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ3 ?12334 ? ? -0.115 ? ? 12.011 ? ; qtot -0.115
?12335 ? ? ?HGR61 ? ?617 ? ?PAR ? ?HQ3 ?12335 ? ? ?0.115 ? ? ?1.008 ? ; qtot 0
?12336 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ2 ?12336 ? ? -0.115 ? ? 12.011 ? ; qtot -0.115
?12337 ? ? ?HGR61 ? ?617 ? ?PAR ? ?HQ2 ?12337 ? ? ?0.115 ? ? ?1.008 ? ; qtot 0
?12338 ? ? CG2R61 ? ?617 ? ?PAR ? ?CQ4 ?12338 ? ? ? 0.11 ? ? 12.011 ? ; qtot 0.11
?12339 ? ? ?OG311 ? ?617 ? ?PAR ? ?OQ1 ?12339 ? ? ?-0.53 ? ?15.9994 ? ; qtot -0.42
?12340 ? ? ? HGP1 ? ?617 ? ?PAR ? ?HQ1 ?12340 ? ? ? 0.42 ? ? ?1.008 ? ; qtot 0
;?residue 618 PAR rtp PAR ?q ?0.0?;?????? Is this correct or I should change this line to ?residue 618 DUM rtp DUM ?q ?0.0??????
?12341 ? ? ?CG331 ? ?618 ? ?PAR ? ?CQ8 ?12341 ? ? ?-0.27 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12342 ? ? ? HGA3 ? ?618 ? ?PAR ? ?HQ7 ?12342 ? ? ? 0.09 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12343 ? ? ? HGA3 ? ?618 ? ?PAR ? ?HQ8 ?12343 ? ? ? 0.09 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12344 ? ? ? HGA3 ? ?618 ? ?PAR ? ?HQ9 ?12344 ? ? ? 0.09 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12345 ? ? ?CG2O1 ? ?618 ? ?PAR ? ?CQ7 ?12345 ? ? ? 0.52 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12346 ? ? ?OG2D1 ? ?618 ? ?PAR ? ?OQ2 ?12346 ? ? ?-0.52 ? ?15.9994 ? ?DUM ? ? ? ? ?0 ? ?15.9994
?12347 ? ? ?NG2S1 ? ?618 ? ?PAR ? ?NQ1 ?12347 ? ? ?-0.47 ? ? 14.007 ? ?DUM ? ? ? ? ?0 ? ? 14.007
?12348 ? ? ? HGP1 ? ?618 ? ?PAR ? ?HQ6 ?12348 ? ? ? 0.33 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12349 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ1 ?12349 ? ? ? 0.14 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12350 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ6 ?12350 ? ? -0.115 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12351 ? ? ?HGR61 ? ?618 ? ?PAR ? ?HQ5 ?12351 ? ? ?0.115 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12352 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ5 ?12352 ? ? -0.115 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12353 ? ? ?HGR61 ? ?618 ? ?PAR ? ?HQ4 ?12353 ? ? ?0.115 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12354 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ3 ?12354 ? ? -0.115 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12355 ? ? ?HGR61 ? ?618 ? ?PAR ? ?HQ3 ?12355 ? ? ?0.115 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12356 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ2 ?12356 ? ? -0.115 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12357 ? ? ?HGR61 ? ?618 ? ?PAR ? ?HQ2 ?12357 ? ? ?0.115 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008
?12358 ? ? CG2R61 ? ?618 ? ?PAR ? ?CQ4 ?12358 ? ? ? 0.11 ? ? 12.011 ? ?DUM ? ? ? ? ?0 ? ? 12.011
?12359 ? ? ?OG311 ? ?618 ? ?PAR ? ?OQ1 ?12359 ? ? ?-0.53 ? ?15.9994 ? ?DUM ? ? ? ? ?0 ? ?15.9994
?12360 ? ? ? HGP1 ? ?618 ? ?PAR ? ?HQ1 ?12360 ? ? ? 0.42 ? ? ?1.008 ? ?DUM ? ? ? ? ?0 ? ? ?1.008

This is like introducing two type for the same residue, right? So I thought that I dont need to change the rtp file ...
I dont know how to modify the bonds, angles and dihedral section because I already have the bond between atoms of PAR molecule:

[ bonds ]
; ?ai ? ?aj funct ? ? ? ? ? ?c0 ? ? ? ? ? ?c1 ? ? ? ? ? ?c2 ? ? ? ? ? ?c3
? ? 1 ? ? 2 ? ? 1
? ? 1 ? ? 3 ? ? 1
? ? 1 ? ? 4 ? ? 1
? ? 1 ? ? 5 ? ? 1
? ? 5 ? ? 6 ? ? 1
? ? 5 ? ? 7 ? ? 1
? ? 7 ? ? 8 ? ? 1
? ? 7 ? ? 9 ? ? 1
? ? 9 ? ?10 ? ? 1

And could you please tell me which other file, I need to modify?
residuetype.dat? aminoacid.rtp ? or other things?
?I read the manual but I still have problem to modify the top file.


Many thanks as always
G.

[Björn Sommer]

Date: Wed, 15 Jan 2014 06:44:22 -0800 (PST)
From: Golshan Hejazi <golshan.hejazi at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Introducing DUMMY atom and top file modification
<1389797062.81229.YahooMailNeo at web140605.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi everyone,
I wanna perform a TI using gromacs. For that I am modifying the top file in order to introduce dummy atoms and I am using charmm ff. I have already introduced a new molecule named PAR and I want to have another molecule in my simulation which is the PAR molecule turned to a DUMMY molecule.

Hi Golshan,

I do not know, if this will help. First, I know that the OPM database uses DUMMY atoms to indicate the top and bottom side of membranes. For that, they use a PDB file which contains "DUM" Atom entries, e.g.

HETATM 4986 O DUM 4986 44.000 10.000 15.700

http://opm.phar.umich.edu

Maybe it would make sense, to keep this notation also for you and maybe you will find somebody who had a similar idea for this kind of protein structures. They are often used for simulations, but I think, usually the DUM atoms are removed prior simulation.

Second, a first search concerning this topic returned this entry:

http://gromacs.5086.x6.nabble.com/dummy-atoms-td4393866.html

It is a similar problem, maybe it provides you some hints.

Best,
Bj?rn

[Golshan Hejazi]

Thanks Bjorn,
These are all good info and for sure helpful. However, I am thinking there should be some easier way in GROMACS because there is "typeB ? ?chargeB ??" feature in gromacs top file which seems to be related to the B-state when doing thermodynamics integration.?
But I could not find any documentation how to modify it for charmm force field. this page for example is showing how to do it for a gromacs force field:?

http://compbio.biosci.uq.edu.au/education/Free-Energy_Course/2.hydration-fe.html


I dont know how to modify the "bond, angle and dihedral" section!

Thanks
G.

Date: Wed, 15 Jan 2014 06:44:22 -0800 (PST)
From: Golshan Hejazi <golshan.hejazi at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Introducing DUMMY atom and top file modification
??? <1389797062.81229.YahooMailNeo at web140605.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi everyone,
I wanna perform a TI using gromacs. For that I am modifying the top file in order to introduce dummy atoms and I am using charmm ff. I have already introduced a new molecule named PAR and I want to have another molecule in my simulation which is the PAR molecule turned to a DUMMY molecule.

Hi Golshan,

I do not know, if this will help. First, I know that the OPM database uses DUMMY atoms to indicate the top and bottom side of membranes. For that, they use a PDB file which contains "DUM" Atom entries, e.g.

HETATM 4986? O? DUM? 4986? ? ? 44.000? 10.000? 15.700

http://opm.phar.umich.edu

Maybe it would make sense, to keep this notation also for you and maybe you will find somebody who had a similar idea for this kind of protein structures. They are often used for simulations, but I think, usually the DUM atoms are removed prior simulation.

Second, a first search concerning this topic returned this entry:

http://gromacs.5086.x6.nabble.com/dummy-atoms-td4393866.html

It is a similar problem, maybe it provides you some hints.

Best,
Bj?rn

[Justin Lemkul]

Post by Golshan Hejazi
Thanks Bjorn,
These are all good info and for sure helpful. However, I am thinking there should be some easier way in GROMACS because there is "typeB chargeB " feature in gromacs top file which seems to be related to the B-state when doing thermodynamics integration.
http://compbio.biosci.uq.edu.au/education/Free-Energy_Course/2.hydration-fe.html
I dont know how to modify the "bond, angle and dihedral" section!

The format is not force field-specific. See manual section 5.7.4 for an
example. B-state parameters can be listed in the same way as the A-state
parameters. For bonds:

ai aj func b0_A kb_A b0_B kb_B

etc.

Explicit B states are only necessary for transforming molecules; they are no
longer necessary for hydration free energies as shown in the tutorial linked above.

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

Justin A. Lemkul, Ph.D.
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 | [phone]

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

[Golshan Hejazi]

Thanks Bjorn,
These are all good info and for sure helpful. However, I am thinking there should be some easier way in GROMACS because there is "typeB ? ?chargeB ??" feature in gromacs top file which seems to be related to the B-state when doing thermodynamics integration.?
But I could not find any documentation how to modify it for charmm force field. this page for example is showing how to do it for a gromacs force field:?

http://compbio.biosci.uq.edu.au/education/Free-Energy_Course/2.hydration-fe.html


I dont know how to modify the "bond, angle and dihedral" section!

Thanks
G.

Date: Wed, 15 Jan 2014 06:44:22 -0800 (PST)
From: Golshan Hejazi <golshan.hejazi at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Introducing DUMMY atom and top file modification
??? <1389797062.81229.YahooMailNeo at web140605.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi everyone,
I wanna perform a TI using gromacs. For that I am modifying the top file in order to introduce dummy atoms and I am using charmm ff. I have already introduced a new molecule named PAR and I want to have another molecule in my simulation which is the PAR molecule turned to a DUMMY molecule.

Hi Golshan,

I do not know, if this will help. First, I know that the OPM database uses DUMMY atoms to indicate the top and bottom side of membranes. For that, they use a PDB file which contains "DUM" Atom entries, e.g.

HETATM 4986? O? DUM? 4986? ? ? 44.000? 10.000? 15.700

http://opm.phar.umich.edu

Maybe it would make sense, to keep this notation also for you and maybe you will find somebody who had a similar idea for this kind of protein structures. They are often used for simulations, but I think, usually the DUM atoms are removed prior simulation.

Second, a first search concerning this topic returned this entry:

http://gromacs.5086.x6.nabble.com/dummy-atoms-td4393866.html

It is a similar problem, maybe it provides you some hints.

Best,
Bj?rn