[gmx-users] pdb2gmx charmm topology lipid
ram bio
rmbio861 at gmail.com
Thu Oct 13 21:51:51 CEST 2011
Dear Justin,
Thanks for the suggestions.
> The lipids are built into the CHARMM27 implementation in Gromacs. You can
> generate their topology with pdb2gmx. Run pdb2gmx on a single lipid,
> convert it to an .itp file, and #include it in the topology.
I separated out one lipid from the POPC bilayer (250 lipids) i am
having (attached -popc.pdb) and modified (popcatomtype.pdb) the atom
names as per the
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp file. Then
i executed
pdb2gmx -f popcatomtype.pdb -o popcatom.gro
choosing option 8 for Charmm ff
&1 for water model
but, i am getting an error as below:
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading popcatomtype.pdb...
Read 52 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 0 residues with 52 atoms
chain #res #atoms
1 'C' 1 52
WARNING: there were 0 atoms with zero occupancy and 52 atoms with
occupancy unequal to one (out of 52 atoms). Check your pdb file.
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 41
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 45
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 57
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 61
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.30#
Processing chain 1 'C' (52 atoms, 1 residues)
There are 1 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue POP0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581
Fatal error:
Residue 'POP' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Please let me know your suggestions to fix this error.
Thanks,
Pramod
On Wed, Oct 12, 2011 at 8:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks.
>>
>> The POPC bilayer i am using is with berger lipids, corrected for dihedrals
>> so as to be compatible with the OPLS FF for aminoacids.
>>
>
> I think significantly more parameters than just dihedrals need to be altered
> to make the Berger united-atom force field compatible with OPLS.
>
>> While searching for the literature on compatibility of lipid FF and
>> protein FF, I found few references where similar modification was done for
>> DOPC lipid bilayer and were suitable with various FF for proteins and also
>> with CHARMM FF:
>>
>> 1. Membrane protein simulations with a united-atom lipid and all-atom
>> protein model: lipid–protein interactions, side chain transfer free energies
>> and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234
>>
>> 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force
>> Fields.J Comput Chem 32: 1400–1410, 2011.
>>
>> I don't have the lipid bilayer with their itp files with CHARMM FF
>> parameterization. Please could you inform me where to obtain them, so that i
>> can use the lipid bilayer structure for embedding the protein and use the
>> related CHARMM FF parameterised itp in the topology file in gromacs for MD
>> simulation.
>>
>
> The lipids are built into the CHARMM27 implementation in Gromacs. You can
> generate their topology with pdb2gmx. Run pdb2gmx on a single lipid,
> convert it to an .itp file, and #include it in the topology. The CHARMM36
> force field is also available in the User Contributions section of the
> Gromacs website.
>
> -Justin
>
>> Thanks in advance,
>>
>> Pramod
>>
>>
>> On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> ram bio wrote:
>>
>> 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.
>>
>>
>> You shouldn't mix and match force fields. Suitable CHARMM lipid
>> parameters are widely available.
>>
>>
>> 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.
>>
>>
>> CHARMM does not use charge groups. Therefore, each atom should be
>> its own "group" in the topology. Using -nochargegrp overrides the
>> default behavior of the .rtp files (which has multi-atom charge
>> groups, although I think this was changed somewhere along the way,
>> but I don't remember if it was before or after 4.5.4).
>>
>> -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> | (540) 231-9080
>> <tel:%28540%29%20231-9080>
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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