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.
On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul <[email protected]> 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 | (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: [email protected] ([email protected] or [email protected]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
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