[gmx-users] Re: pdb2gmx charmm topology lipid

[Justin A. Lemkul]

ram bio wrote:
> 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.
> 

The answers to nearly every error message are listed either on the Gromacs 
website or in the list archive.  For instance, this happens to be one of the 
most common:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Check the .rtp file for the expected name.

-Justin

-- 
========================================

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

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