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

[Justin A. Lemkul]

Oliver Grant wrote:
> 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! :)

Combining different force fields into a single system completely invalidates it, 
so yes, I'd say you're doing something wrong :)

-Justin

> 
>  ;
> ;    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 <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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