Hi Leila,
Your N terminus needs to have the valence filled on the N (thus the hydrogen
added) and the valence of the C at the end should also be filled. You can
also delete all the CONECT records in your pdb file. Leap should take care
of the connectivity. I think they should be called NGLY and CGLY but that
may have changed.
Oliver ;)
On 7 December 2010 14:40, 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>
> 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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>
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Received on Tue Dec 07 2010 - 07:30:02 PST
