[gmx-users] Re: Problem with using topolbuild1_3.tgz
Sweta Iyer
iyer at wehi.EDU.AU
Sat Jan 22 07:44:25 CET 2011
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> Today's Topics:
>
> 1. OPLS implicit solvent problems (francesca.stanzione at unina.it)
> 2. Re: OPLS implicit solvent problems (Per Larsson)
> 3. (no subject) (francesca.stanzione at unina.it)
> 4. CG to FG transformation error (Anirban Ghosh)
> 5. Re: Problem with using topolbuild1_3.tgz (Bruce D. Ray)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Jan 2011 13:51:08 +0100
> From: francesca.stanzione at unina.it
> Subject: [gmx-users] OPLS implicit solvent problems
> To: gmx-users at gromacs.org
> Message-ID: <20110121135108.kg4c6rbjr44kgc0k at webmail.unina.it>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Hello,
>
> I try to perform an implicit solvent simulation with Gromacs 4.5.3.
> version. I have a system corresponding to 6 peptides generated by
> Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA
> and i put the N-and C- termini as NH2 and COOH. My topology file is
> correct, and is all systems are included.
>
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is
> included gbsa.itp
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
>
> ; Include water topology
> #include "./oplsaa.ff/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 topology for ions
> #include "./oplsaa.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> Protein_chain_C 1
> Protein_chain_D 1
> Protein_chain_E 1
> Protein_chain_F 1
> -----------------------------------------------------------------------------
>
> When I start my simulations (md_start.mdp) in implicit solvent, i
> have this fatal error:
>
> GB parameter(s) missing or negative for atom type 'opls_912B'
>
> GB parameter(s) missing or negative for atom type 'opls_267'
>
> GB parameter(s) missing or negative for atom type 'opls_269'
>
> GB parameter(s) missing or negative for atom type 'opls_268'
>
> GB parameter(s) missing or negative for atom type 'opls_270'
>
> Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1123
>
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 5 atomtypes or they might be
> negative.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors.
>
> ----------------------------------------------------------------------------
>
> Controlling these atoms they corresponding to:
>
> opls_912B= the CA of N-terminal residue
>
> opls_267= Co in COOH
>
> opls_268= Oh in COOH
>
> opls_269= Oc in COOH neutral
>
> opls_270= H in COOH
>
> ----------------------------------------
>
> in the file gbsa.itp in opls.ff directory these atoms missing. Now,
> have I done something wrong? If is all ok, is it possible to create
> these missing atoms in the gbsa.itp file?
>
> thanx,
>
> francesca stanzione
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> ------------------------------
>
> Message: 2
> Date: Fri, 21 Jan 2011 14:11:40 +0100
> From: Per Larsson <per.larsson at sbc.su.se>
> Subject: Re: [gmx-users] OPLS implicit solvent problems
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <6EC741E6-55F1-41C0-B67A-BC133AB22947 at sbc.su.se>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi!
>
> Thanks for pointing this out.
> It is unfortunate that they are missing from the gbsa.itp-file. I will add
> them, but I do not have time today.
> If you want to get going, you can add them yourself.
> The gb-parameters are essentially based on atom hybridization, so for each
> missing atom you find another that has the same (sp, sp2,sp3)
> hybridization, and add it to the gbsa.itp-file.
>
> Cheers
> /Per
>
> 21 jan 2011 kl. 13.51 skrev francesca.stanzione at unina.it:
>
>> Hello,
>>
>> I try to perform an implicit solvent simulation with Gromacs 4.5.3.
>> version. I have a system corresponding to 6 peptides generated by Pymol
>> with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put
>> the N-and C- termini as NH2 and COOH. My topology file is correct, and
>> is all systems are included.
>>
>> ; Include forcefield parameters
>> #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is
>> included gbsa.itp
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #include "topol_Protein_chain_B.itp"
>> #include "topol_Protein_chain_C.itp"
>> #include "topol_Protein_chain_D.itp"
>> #include "topol_Protein_chain_E.itp"
>> #include "topol_Protein_chain_F.itp"
>>
>> ; Include water topology
>> #include "./oplsaa.ff/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 topology for ions
>> #include "./oplsaa.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein
>>
>> [ molecules ]
>> ; Compound #mols
>> Protein_chain_A 1
>> Protein_chain_B 1
>> Protein_chain_C 1
>> Protein_chain_D 1
>> Protein_chain_E 1
>> Protein_chain_F 1
>> -----------------------------------------------------------------------------
>>
>> When I start my simulations (md_start.mdp) in implicit solvent, i have
>> this fatal error:
>>
>> GB parameter(s) missing or negative for atom type 'opls_912B'
>>
>> GB parameter(s) missing or negative for atom type 'opls_267'
>>
>> GB parameter(s) missing or negative for atom type 'opls_269'
>>
>> GB parameter(s) missing or negative for atom type 'opls_268'
>>
>> GB parameter(s) missing or negative for atom type 'opls_270'
>>
>> Program grompp, VERSION 4.5.3
>> Source code file: grompp.c, line: 1123
>>
>> Fatal error:
>> Can't do GB electrostatics; the implicit_genborn_params section of the
>> forcefield is missing parameters for 5 atomtypes or they might be
>> negative.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors.
>>
>> ----------------------------------------------------------------------------
>>
>> Controlling these atoms they corresponding to:
>>
>> opls_912B= the CA of N-terminal residue
>>
>> opls_267= Co in COOH
>>
>> opls_268= Oh in COOH
>>
>> opls_269= Oc in COOH neutral
>>
>> opls_270= H in COOH
>>
>> ----------------------------------------
>>
>> in the file gbsa.itp in opls.ff directory these atoms missing. Now, have
>> I done something wrong? If is all ok, is it possible to create these
>> missing atoms in the gbsa.itp file?
>>
>> thanx,
>>
>> francesca stanzione
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>
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>
> Message: 3
> Date: Fri, 21 Jan 2011 14:44:17 +0100
> From: francesca.stanzione at unina.it
> Subject: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20110121144417.v2czlcmrbk8kkogs at webmail.unina.it>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Hi Pers,
>
> thank you for reply. I'm trying to add these missing atoms with
> your guideline, but I don't know if all parameters that I'm going to
> add are corrects. When you have a time, can you add these missing
> atoms in the program or can you help me to create a correct
> substitution of these atoms? Because I can try to add the parameters
> in the five coloumns present but I should know if these values are
> right.
>
> thanks,
>
> francesca
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> ------------------------------
>
> Message: 4
> Date: Fri, 21 Jan 2011 19:17:47 +0530
> From: Anirban Ghosh <reach.anirban.ghosh at gmail.com>
> Subject: [gmx-users] CG to FG transformation error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>, Anirban
> Ghosh <reach.anirban.ghosh at gmail.com>
> Message-ID:
> <AANLkTin9wesqMTv_LFo_4ERQxoDgpk6v802v85-3Wy5_ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I am trying to convert a coarse grained protein to a full atom model after
> CGMD. I am using the modified gromacs_reverse code available from MARTINI
> site. I am using the following command:
>
> g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro
>
> But in the output full.gro all the atoms are having coordinate values as
> "0.00".
>
> My pro_cg.top file looks like:
>
> #define _FF_GROMOS96
> #define _FF_GROMOS42A2
> ;#define _FF_GROMACS
> ;#define _FF_GROMACS1
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 1 yes 0.125 0.5
>
>
> #include "ffG43a2nb.itp"
> #include "ffG43a2bon.itp"
>
>
> Is this correct? where I am going wrong? I think the problem is with
> pro_cg.top file only.
>
> Any suggestion is welcome.
>
>
> Thanks,
>
>
> -Anirban
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> ------------------------------
>
> Message: 5
> Date: Fri, 21 Jan 2011 06:55:30 -0800 (PST)
> From: "Bruce D. Ray" <brucedray at yahoo.com>
> Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz
> To: gmx-users at gromacs.org
> Message-ID: <417950.70449.qm at web35801.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <iyer at wehi.EDU.AU> wrote:
>> Hi, I am trying to generate topology files for a set of lipids with the
>> help of topolbuild1_3.tgz package found at the other software page of
>> GROMACS website.
>>
>> I downloaded and installed all files and tried running the program with
>> a
>> MOL2 file with charges in it. However, it shows an error message as
>> follows:
>>
>> Fatal error.
>> Source code file: readmol2.c, line: 758
>> Atom 1 (C) has 3 connections when allowed 0
>>
>> I am not sure how to get over this problem! Wonder what will fix this
>> error and get the program running!
>
> A major requirement of topolbuild is that the mol2 file use correct atom
> types as defined by Tripos, whose file format mol2 is, and as used in
> Sybyl.
> The error message suggests that you have not specified correct Tripos
> Sybyl
> atom types. There may be other problems in your mol2 file as well.
> Correct the atom types and check that the file is otherwise syntactically
> correct and it should work.
>
> However, I believe that lipid topology files for gromacs are already
> available
> for download.
>
> I hope that helps.
>
>
> --
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN 46202-3273
Hi Bruce,
Thanx for the reply. The MOL2 file was generated by the RESP ESP charge
derive server. I did not check the file in SYBYL. However, structurally it
seems correct. I will try reading it into sybyl and then resave it into
another mol2 file.
I am looking at making topology files for lipids like cardiolipin, di
myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and
myristoleic acid. DO you know of any available gromacs topology files for
these?
Cheers
Sweta
>
>
>
>
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