Alberto Sergio Garay wrote:
Dear David (van der Spoel)
Thank you for your time.
Firstly: I don't need to add any H atom to my polymer. All atoms that I
need are in the rtp topology file. So I did not change the hdb file.
Using this command (as you suggested in the last message):
pdb2gmx -ignh -ter -f polymer.gro -p top
Below I extracted the main differences with the previous pdb2gmx error:
Processing chain 1 (239 atoms, 14 residues)
Fatal error:
Atom O in residue VBT 2 not found in rtp entry with 24 atoms
while sorting atoms
This still looks like it is doing something to your termini, or you
could have an error in the rtp file. Can you try to make a minimal
system and post it to the list?
Evidently, pdb2gmx is doing something funny with my polymer, because it
found 239 atoms in my gro file, when it really contains 309. Without the
option -ignh (as I did it before) it found the correct number of atoms
(309).
Finally it also found the atom O in my gro files, which (again) it
doesn't really exist.
What is pdb2gmx doing? I don't understand what I am doing wrong.
Any suggestion will be appreciated.
Sergio
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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