[gmx-users] Re: OPLS-AA/L force field
Oliver Grant
olymacfoogal at gmail.com
Thu May 20 13:48:19 CEST 2010
The force fields have to be compatible but this way works fine.
On 19 May 2010 12:50, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>
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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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