RAJAVARMAN.K wrote:
Respected sir,
am working with gold cluster .am planing to simulate
gold cluster in the presence of vacuum.but i can,t able
to convert the pdb file into gro,top format caz of the
following statement" Residue '2' not found in residue
topology database ".
i already gone through gromacs mailing list as well as
gromacs manual 5 chapter.but i really don't know what
to change in .rtp,.top files. so plz help me .am
attaching my error statement as well as input
file.already have experience in working with
protein,peptides,domain.but this is first time am
using metal cluster ( i.e 40 atoms of gold).can u
please kindly help me by creating gold cluster
topology,gro file.
It's great that you've gone to the trouble of looking through some
useful material before asking your question. It would also be good to
capitalize relevant words and refrain from using non-standard
abbreviations like "caz" and "plz". You're asking for free help from
busy people, so you should follow business-like communication styles.
Doing this shows that you care enough about your problem to communicate
well, and thus it might be more worth our time to help you.
There's some useful background reading available here
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
The problem comes when your coordinate file is using "2" in the place
where pdb2gmx is expecting a residue name found in an .rtp file it
already knows about. Unless you have a force field .rtp already
installed that's suitable for gold clusters, you are probably using the
wrong tool to generate a .top file. I'd expect to have to make one by
hand, and there's really no other option than to sit down with Chapter 5
of the manual and the paper that describes your force field and be
prepared to work hard.
Mark
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