[gmx-users] Re: OPLS-AA/L force field
Oliver Grant
olymacfoogal at gmail.com
Thu May 20 14:18:20 CEST 2010
*I guess that depends on what you mean by "works fine." *
I mean the method of using pdb2gmx to generate a top and gro and then
appending the gro files and including the .itp files in the .top file, works
if you want to use two force fields. Originally I thought that was the
question.
*I guess it all depends on what you mean (below) by "non amber force field"*
I'm using GLYCAM06, so it involves a bit more effort to generate a .top and
.gro file than just using pdb2gmx but I thought I'd leave it out as I just
wanted to explain the method I use to include it. Apologies for the
confusion!
Oliver
-Justin
On 20 May 2010 13:00, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Oliver Grant wrote:
>
>> The force fields have to be compatible but this way works fine.
>>
>>
> I guess that depends on what you mean by "works fine." If you mean that
> you can produce a stable simulation, then yes, it may "work," but I would
> question the underlying premise of combining different force fields. If,
> for example, you're using an AMBER force field for, say, a protein, and OPLS
> for a small molecule, then what you're doing is wrong. The combination
> rules required by both force fields are different, as are the underlying
> derivation schemes and quite possibly some more details I'm not thinking
> about at the moment.
>
> I guess it all depends on what you mean (below) by "non amber force field"
> and how different it is from the actual requirements of the AMBER force
> field you're using. If this "non amber force field" was designed to be
> compatible with your chosen force field, and there was some suitable
> derivation scheme involved, then things will probably work. If you're
> mixing and matching parameter sets, be prepared for very tough questions
> from any reviewers who see your work.
>
> -Justin
>
> On 19 May 2010 12:50, Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> 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>
>> <mailto: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 <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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