안세나 wrote:
Dear gmx-usr
I would like to make *.top with the myoglobin pdb file which contain CO
ligand like this form.
HETATM 1268 C CMO 155 35.753 5.930 11.242 0.77 12.30
1MLF1367
HETATM 1269 O CMO 155 35.946 6.791 11.935 0.77 12.70
1MLF1368
However, this pdb file regards CO ligand as CMO residue, so I added the
information
for CMO residue to ffG43a1.rtp (I used 0 forcefield.) like this.
[CMO]
[atoms]
C C 0.383 0
O O -0.383 0
[bonds]
C O
And, I also added CMO residue to aminoacids.dat.
But, the result of pdb2gmx said "Atom CA cannot found in residue CMO156
while adding hydrogen.
What's the problem?
Is it right to use rtp file, if not, should I make *.itp file regarding
CO ligand as a molecule?
Please tell me the answer. Thank you.
give the molecule another chain label. pdb2gmx thinks it is part of the
polypeptide chain. make sure to use the -ter flag
Bye,
Sena
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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