Hello,
On Tue, Dec 7, 2010 at 9:40 AM, leila karami <karami.leila1.gmail.com>wrote:
> 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>
>
These messages mean that atoms from the template residues CGLY and NGLY (C-
and N-terminal glycines) were not found in the PDB, so they were added.
This is normal.
> Illegal CONECT record in pdb file
> Illegal CONECT record in pdb file
>
This means that leap found CONECT records in the PDB that didn't make
sense. Leap will listen to connect records in the PDB that make sense to it
(i.e. CONECT records indicating a disulfide bond in the system). You should
visualize your generated prmtop / coordinate file to make sure the topology
of your system appears correct.
Good luck!
Jason
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 08 2010 - 06:30:03 PST
