[gmx-users] mktop
ram bio
rmbio861 at gmail.com
Wed Oct 12 22:53:16 CEST 2011
Dear Justin,
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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