[gmx-users] mktop/swissparam
ram bio
rmbio861 at gmail.com
Wed Oct 12 22:54:25 CEST 2011
> Thanks, and I accept your suggestions;
>
> If SwissParam was designed to be used with CHARMM, the most intuitive next
> step is to use CHARMM for the MD, is it not?I understand the point about
> trying to keep the force fields consistent between docking and MD, but it
> may not be feasible (i.e., there may not be suitable parameters in OPLS for
> the bizarre functional groups you're dealing with).
>
> Yes, I also tried CHARMM FF to generate the topology file of the protein
> using pdb2gmx (without ligand), and as per the swissparam and gromacs
> tutorial i could build the protein-ligand-lipid bilayer and minimize it
> using mdrun and and i am at the NPT equilibration step, everything is ok
> with this procedure and without errors, but my lipid bilayer is made up of
> POPC and the POPC itp file has OPLS FF topologies. So, i was wondering
> whether the POPC itp file i am using for MD simulations can be used with the
> protein and ligand topology file generated by CHARMM.
>
> and as per the swissparam tutorial the command to generate topology file
> for protein is:
>
> pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
>
>
>
> in the gromacs 4.5.4 version the option to select Charmm FF from the
> pdb2gmx command is available, but i could not understand the usage of
> -nochargegp flag as per the tutorial, is this flag still valid while
> generating toplogies.
>
> Please let me know your comments and suggestions regarding the procedure
> followed and the itp files usage for gromacs MD simulations.
>
> Thanks in advance,
>
> Pramod
>
>
>
> On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> ram bio wrote:
>>
>>> Dear Justin,
>>>
>>> As i generated the protein-ligand docked complex using opls FF, for the
>>> consistency, i am trying to use opls ff generated ligand parameters during
>>> md simulations in lipid bi layer. I found that MKTOP can generate topology
>>> files using opls ff for small molecules.
>>>
>>>
>> I understand that. The program did a poor job, per the reasons I cited
>> before. I do not know anything about mktop (other than what it does), so I
>> cannot analyze its suitability here, but due to missing parameters and bogus
>> charges, you should not use that topology for anything.
>>
>>
>> I have also tried swiss param to generate the ligand parameters to be
>>> used in protein ligand simulation using gromacs. The force field i am using
>>> for simulations is OPLS. My ligand contains an azido group and a tropane
>>> ring with protonated nitrogen. SwissParam force field has been designed to
>>> be compatible with the Charmm force field, but they are not tested on
>>> opls.Using the ligand topologies from swissparam, i was able to run the MD
>>> simulations using gromacs with opls without errors (swissparam - gromacs
>>> tutorial), only issues being the charges on the ligand, so i generated
>>> various input files (mol2 files) for swissparam with charges generated
>>> using ambcc1, gastergier and MMFF. But the itp files obtained from
>>> swissparam had same charges for the ligand atoms irrespective of the input
>>> provided i.e. charged or uncharged mol2 files, and
>>>
>>>
>> If SwissParam was designed to be used with CHARMM, the most intuitive next
>> step is to use CHARMM for the MD, is it not? I understand the point about
>> trying to keep the force fields consistent between docking and MD, but it
>> may not be feasible (i.e., there may not be suitable parameters in OPLS for
>> the bizarre functional groups you're dealing with).
>>
>> As per Gromacs website:
>>>
>>> "Note that an .itp file <http://www.gromacs.org/**
>>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
>>> will be specific to a given force field, and will only function when
>>> included by a .top file <http://www.gromacs.org/**
>>> Documentation/File_Formats/.**top_File<http://www.gromacs.org/Documentation/File_Formats/.top_File>>
>>> that has previously included the .itp files <http://www.gromacs.org/**
>>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
>>> for that force field. Appropriate use of the |#define| and |#ifdef|
>>> mechanisms can permit the same .itp file <http://www.gromacs.org/**
>>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>>
>>> to work with multiple force fields, e.g. |share/top/water.itp|."
>>>
>>>
>> Note the key caveat here - through the use of #define and #ifdef you can
>> make use of different force fields. That means you can control which
>> parameters are applied based on different conditions. I could write an .itp
>> file for any molecule that has force field parameters for any force field,
>> and all I'd have to do is enclose all relevant directives within #ifdef
>> blocks and it would work. This note does *not* indicate that you can mix
>> and match force fields. Doing so is generally a very bad idea, if it even
>> works syntactically.
>>
>>
>> so, i think even though the swissparam generated topologies based on MMFF
>>> fit to charmm (based on testing), they could also be used with opls. It was
>>> informed by swiss param team that the ligand parameters generated by
>>> swissparam could also be used with opls FF in principle as they are based on
>>> MMFF
>>> So, in order to cross check or validate my results i was trying to use
>>> mktop to generate the ligand topologies for MD simulations.
>>>
>>>
>> Maybe the SwissParam-generated topology will work. There are
>> commonalities underlying these force fields, to be sure. Still, the
>> methodology for properly deriving OPLS parameters is quite well described in
>> the literature, right down to the QM basis sets required to run the geometry
>> optimizations and charge calculations.
>>
>> -Justin
>>
>> Please let me know your comments and suggestions on the procedure ,
>>> regarding the compatibility of MMFF generated topologies to be used by OPLS
>>> and other methods to validate my results.
>>>
>>> Thanks,
>>>
>>> Pramod
>>>
>>> On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>> ram bio wrote:
>>>
>>> Dear Justin,
>>>
>>> Thanks for the information.
>>>
>>> Initially, i just wanted to run a simulation of protein-ligand
>>> in water solvent . I renamed the topology.top generated from
>>> mktop to ligand.itp; and included the ligand.itp line in the
>>> topol.top file generated from the pdb2gmx. During the pdb2gmx
>>> command, i used opls FF. The coordinates of ligand used as
>>> input for mktop were added to the output of pdb2gmx (process.pdb
>>> - only protein coordinates), so that the structure file along
>>> with ligand coordinates (processlig.pdb) can be used for further
>>> steps. I doubt whether the procedure followed by me is correct,
>>> as when i execute grompp command to add ions i am getting errors :
>>>
>>>
>>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
>>>
>>>
>>> ERROR 1 [file ligand.itp, line 291]:
>>> No default Ryckaert-Bell. types
>>>
>>> ..........
>>>
>>> ------------------------------**__-------------------------
>>>
>>> Program grompp, VERSION 4.5.4
>>> Source code file: toppush.c, line: 1526
>>>
>>> Fatal error:
>>> [ file ligand.itp, line 397 ]:
>>> Atom index (0) in dihedrals out of bounds (1-53).
>>> This probably means that you have inserted topology section
>>> "dihedrals"
>>> in a part belonging to a different molecule than you intended to.
>>> In that case move the "dihedrals" section to the right molecule.
>>> For more information and tips for troubleshooting, please check
>>> the GROMACS
>>> website at http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors>
>>> <http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>>> >
>>> ------------------------------**__-------------------------
>>>
>>>
>>> The commands executed to reach the grompp step are as follows:
>>>
>>>
>>> pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb
>>> editconf -f processlig.pdb -o procent.pdb -princ
>>> editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic
>>> genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p
>>> topol.top
>>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr
>>>
>>> I have attached the topol.top, ligand.itp and procentsolv.gro
>>> files for your information, Please let me know your suggestions
>>> to fix this error.
>>>
>>>
>>> The ligand.itp file is trash. Most of your atoms have zero charge
>>> (except for a few that have +/- 1...yikes!) and on line 397 (as
>>> cited in the error message) atom 0 is referenced, which of course
>>> does not exist, since numbering starts with 1. You also have some
>>> exotic atom types present, and thus bonded parameters cannot be
>>> assigned, as grompp complained earlier.
>>>
>>> You need a better quality topology, and perhaps a different force
>>> field that might be suited for doing these simulations.
>>>
>>> -Justin
>>>
>>> Thanks,
>>> Pramod
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>>
>>>
>>>
>>> ram bio wrote:
>>>
>>> Dear Gromacs Users,
>>>
>>> I am using opls FF for my protein-ligand simulations in
>>> lipid
>>> bilayer. I have generated the topologies for the ligand
>>> using
>>> MKtop. The output from the MKTOP gives the top file, but
>>> not the
>>> coordinate/structure file. Please let me know if any
>>> tutorial is
>>> available for merging the output of mktop into gromacs MD
>>> simulation.
>>>
>>>
>>>
>>> You can #include any molecule topology in a system .top,
>>> provided
>>> you have the right format:
>>>
>>> http://www.gromacs.org/____**
>>> Documentation/File_Formats/.__**__itp_File<http://www.gromacs.org/____Documentation/File_Formats/.____itp_File>
>>> <http://www.gromacs.org/__**Documentation/File_Formats/.__**
>>> itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
>>> >
>>>
>>>
>>> <http://www.gromacs.org/__**
>>> Documentation/File_Formats/.__**itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File>
>>> <http://www.gromacs.org/**Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>
>>> >>
>>>
>>> There is no tutorial for using mktop with a
>>> protein-ligand/membrane
>>> system, but there are tutorials for protein-ligand complexes:
>>>
>>> http://www.bevanlab.biochem.__**__
>>> vt.edu/Pages/Personal/**justin/____gmx-tutorials/**
>>> complex/index.____html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/complex/index.____html>
>>> <http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/**
>>> complex/index.__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
>>> >
>>>
>>>
>>> <http://www.bevanlab.biochem._**_
>>> vt.edu/Pages/Personal/justin/**__gmx-tutorials/complex/index.**__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html>
>>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>>> gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
>>> >>
>>>
>>> and membrane protein systems:
>>>
>>> http://www.bevanlab.biochem.__**__
>>> vt.edu/Pages/Personal/**justin/____gmx-tutorials/**
>>> membrane_____protein/index.**html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/membrane_____protein/index.html>
>>> <http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/**
>>> membrane___protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
>>> >
>>>
>>> <http://www.bevanlab.biochem._**_
>>> vt.edu/Pages/Personal/justin/**__gmx-tutorials/membrane___**
>>> protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html>
>>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>>> gmx-tutorials/membrane_**protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
>>> >>
>>>
>>> -Justin
>>>
>>> -- ==============================**____==========
>>>
>>>
>>>
>>> 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> <http://vt.edu> | (540)
>>> 231-9080 <tel:%28540%29%20231-9080>
>>> <tel:%28540%29%20231-9080>
>>> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>>> >
>>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
>>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >>
>>>
>>> ==============================**____==========
>>>
>>>
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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
>>> <tel:%28540%29%20231-9080>
>>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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