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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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