[gmx-users] Re: OPLS-AA/L force field

[Oliver Grant]

Can you not run pdb2gmx for each of your molecules that you want separate
force fields for? Then cat the gro files, renumber and include the molecule
types as .itp files in the .top file as below. If I'm doing anything wrong
please let me know! :)

 ;
;    This is your topology file
;    "What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"

[ atomtypes ]
------------------------------------------------------------------------------------from
the top file of the non amber force field
;name  bond_type    mass    charge   ptype          sigma      epsilon
CY            CY      0.0000  0.0000  A   3.39967e-01  4.57730e-01
O              O      0.0000  0.0000  A   2.95992e-01  8.78640e-01
HO            HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
H1            H1      0.0000  0.0000  A   2.47135e-01  6.56888e-02
O2            O2      0.0000  0.0000  A   2.95992e-01  8.78640e-01
N              N      0.0000  0.0000  A   3.25000e-01  7.11280e-01
H2            H2      0.0000  0.0000  A   2.29317e-01  6.56888e-02
OY            OY      0.0000  0.0000  A   3.00001e-01  7.11280e-01
HC            HC      0.0000  0.0000  A   2.64953e-01  6.56888e-02
H              H      0.0000  0.0000  A   1.06908e-01  6.56888e-02
C              C      0.0000  0.0000  A   3.39967e-01  3.59824e-01
OS            OS      0.0000  0.0000  A   3.00001e-01  7.11280e-01
CG            CG      0.0000  0.0000  A   3.39967e-01  4.57730e-01
OH            OH      0.0000  0.0000  A   3.06647e-01  8.80314e-01

#include
"protein.itp"------------------------------------------------------------------------------------from
the top file of the amber force field, contains everything usually specified
here under [molecule types].

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_CA
#include "CA_posre.itp"
#endif

#include
"trisacc.itp"------------------------------------------------------------------------------------from
the top file of the non amber force field, contains charges etc.

; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif

; Include water topology
#include "ffamber_tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "Na_amber99sb.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
trisacc            1
SOL         10697
Na          4



2010/5/19 you zou <zou.you at live.com>

>  Hi Justin,
>
> Thank you for your help, But when I run x2top command there is one error
> that is:
> "
> Can not find forcefield for atom C1-1 with 2 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
>
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"
>
> I don't know how can I adjust this error.
> I have one more question again, this command give me a top file, if I want
> gro file of this pdb (drug that has removed from drug-enzyme complex) how
> can I do that?
>
> you zou wrote:
> > Dear Users,
> >
> > I have one question about Drug-Enzyme Complex,Similar to tutorial If I
>
> >
>   want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> > Beta version" server too, or not?
>
> No. You can't use two different force fields in one simulation system.
>
> > If I can't use this server, how can I make .gro file and .itp file for
> > drug that remove from initial .pdb file?
> >
>
> There are several programs in the User Contributions from the website, x2top
>
> (which is distributed with Gromacs), or you can build the topology by hand. No
> matter what you choose, you need a thorough understanding of the mechanics of
> your chosen force field, methods of validation, and of course Chapter 5 in the
>
> Gromacs manual.
>
>
> Thanks
>
>
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