Liu Shiyong wrote:
Thanks.
I used the PDB file with H . It works though it's still a mystery for
me why PDB file without H couldn't work.
Because the atoms will be numbered wrong. When you use pdb2gmx, hydrogens will
be added to some groups (polar groups, aromatics, N-termini, etc). So, starting
with chain A, which now has three additional protons on the N, the numbering
will be very different from the original pdb file. Check out each .pdb file and
your topologies and see for yourself how quickly the numbering differs.
-Justin
On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Liu Shiyong wrote:
<snip>
The problem lies here:
Including chain 1 in system: 1296 atoms 125 residues
Including chain 2 in system: 1274 atoms 123 residues
Including chain 3 in system: 2085 atoms 201 residues
This suggests that chain 2 (Protein B) should contain numbers up to
about 2500.
ATOM 1996 O ASN B 248 49.634 9.874 85.195
1.00 0.00
ATOM 1997 OXT ASN B 248 50.217 10.536 83.158
1.00 0.00
TER
ATOM 1998 N GLY C 249 70.273 30.186 73.098
1.00 0.00
ATOM 1999 CA GLY C 249 68.973 30.327 72.421
1.00 0.00
This is the original .pdb file, then? The hydrogens will be missing
from the appropriate groups in the pdb2gmx-processed output
structures. You can check the numbering (and pertinent charge
groups) in the topology for each chain, to be sure.
make_ndx -f ${df}.pdb -o ${file}.ndx >
${file}.output.make_ndx
<< _EOF_
del 0-9
chain A and B
chain C
q
_EOF_
This should work, with the right input :)
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@ku.edu>)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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