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 <jalem...@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 <jalem...@vt.edu >> <mailto:jalem...@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> >> >> ==============================__========== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/__mailman/listinfo/gmx-users >> <http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> http://www.gromacs.org/__Support/Mailing_Lists/Search >> <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists >> <http://www.gromacs.org/Support/Mailing_Lists> >> >> > > -- > ======================================== > > 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@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 www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
popc.pdb
Description: Protein Databank data
popcatomtype.pdb
Description: Protein Databank data
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