Alberto Sergio Garay wrote:
Dear David
I renamed the atom OT1 to OX1 in the gro and rtp files but pdb2gmx still
gives me the same error:
Processing chain 1 (239 atoms, 14 residues)
There are 7 donors and 13 acceptors
There are 0 hydrogen bonds
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421
Fatal error:
Atom O in residue VBT 2 not found in rtp entry with 24 atoms
while sorting atoms.
It is strange that it found 14 residues (which it is correct) but only
239 atoms (the system has 309 atoms) so it seems that pdb2gmx would have
taken out all the H atoms of the system.
What are the steps that pdb2gmx follows when it works on a molecule?
I will be working on it. Thank you in advance for helping me.
If you use the -ignh flag the you need to recreate hydrogens using the
hydrogen database, If not, then all names in the coordinate file need to
match exactly the rtp file. pdb2gmx also renames atoms according to the
table in xlateat.dat. You may want to generate a file in your working
directory called xlateat.dat which contains just a single zero on the
first line. In this way no atom renaming is done.
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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