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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