Dear amber users
I want to do MD simulation of a protein. I'm using amber03 forcefield.
first and last residues in my pdb (45 residues) are as follows:
HETATM 1 N GLY A 1 2.559 0.333 -17.163
HETATM 2 CA GLY A 1 1.264 0.268 -17.815
HETATM 3 C GLY A 1 0.282 -0.611 -17.680
HETATM 4 O GLY A 1 0.542 -1.260 -15.939
HETATM 5 H GLY A 1 3.358 0.800 -17.630
HETATM 6 2HA GLY A 1 0.858 1.266 -17.883
HETATM 7 3HA GLY A 1 1.661 -0.271 -18.675
.
.
.
.
HETATM 1033 N GLY A 45 10.177 7.703 3.904
HETATM 1034 CA GLY A 45 11.310 8.204 4.661
HETATM 1035 C GLY A 45 12.559 7.370 4.453
HETATM 1036 O GLY A 45 12.493 6.171 4.189
HETATM 1037 H GLY A 45 10.232 6.831 3.461
HETATM 1038 2HA GLY A 45 11.513 9.220 4.355
HETATM 1039 3HA GLY A 45 11.050 8.153 5.718
after loadpdb file:
Created a new atom named: H within residue: .R<NGLY 7>
Added missing heavy atom: .R<CGLY 66>.A<OXT 8>
Illegal CONECT record in pdb file
Illegal CONECT record in pdb file
total atoms in file: 1864
Leap added 4 missing atoms according to residue templates:
1 Heavy
3 H / lone pairs
The file contained 1 atoms not in residue templates
is it normal? or there is problem. if so, how to fix it?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Tue Dec 07 2010 - 07:00:04 PST
