Peyman Yamin wrote:
Hi everyone,
can one still search the mailing list entries? I can't find it in the new
site!
I've posted this several times in the last few days:
http://oldwww.gromacs.org/swish-e/search/search2.php
A question: what would one want to do if he had a PDB file of a dimer and
pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried
to separate two mers and then pdb2gmx'ed them getting nice topologies of each.
But how can I merge them together again? the numbering will be messy. There
should be some more human way for that :-) Editconf does not take two files
and I don't want to put the other one at a random position since it needs to
be just beside the other mer! What should one do at all, if one gets a NMR-
based PDB which has the structure of more than one chemically equal species
and wants to work with it?
Concatenate the files using standard *nix utilities like cat, remove any
repeated/unnecessary box information or REMARK lines, and use genconf to renumber.
-Justin
With Herzian thanks...
Cheers,
Peyman
--
Peyman Yamin
Institut fuer Strukturbiologie und Biophysik (ISB)
ISB-3: Strukturbiochemie
Forschungszentrum Juelich
D-52425 Juelich
Tel: (49)-2461-61-2875
Fax: (49)-2461-61-2023
mailto: p.yamin[at]fz-juelich.de
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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