[gmx-users] Request for PDB with the same label as in Gromocs topologies.
Mikko.Hellgren at mbb.ki.se
Tue Mar 28 16:49:04 CEST 2006
Hi all Gromacs users and developers, I wonder if anybody has pdb files
for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) with the same
labels as in Gromacs topologies. This would save me a lot of time in my
work since the atom names in my PDB for the ligands are different from
Gromacs atom names, and it would take me a lot of time to figure out how
to make them consistent to each other.
I think it would be great if the developers of all the topologies in
Gromacs also could submit the pdb file of the topology. This would save
time (at least to me :-)) and help me to understand what all atom names
in gromacs topologies stand for. I know that the problem of different
atom labels is not due to Gromacs but it is the reason for the need of
pdb:s for all molecules with topologies in Gromacs.
If there is some other way to relabel atom names in an easy fashion, I
would be very great full for any advice on that also.
PhD student at Karolinska Institutet
mikko.hellgren at ki.se <------- if you have the pdb I want, please send it
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