Hello,
You would have to be more specific. What bonds is it creating? Perhaps you
can post a picture, etc, or tell us what atoms are being bonded.
All the best,
Jason
On Sat, Dec 11, 2010 at 6:33 AM, leila karami <karami.leila1.gmail.com>wrote:
> Dear amber users
>
> I did simulation of protein-dna complex by gromacs. I want to do hydrogen
> bond analysis by amber, I know for that I need to .prmtop and .mdcrd files.
> I converted gromacs trajectory file (.xtc) to .mdcrd file by VMD.
>
> I want to create .prmtop and .inpcrd files for my pdb file (containing
> protein + dna + water + Na). I'm using amber03
> forcefield. first and last protein residues in my pdb are as follows:
>
> ATOM 1 N GLY 1 26.110 41.200 17.610 1.00 0.00
> ATOM 2 CA GLY 1 24.840 40.900 18.290 1.00 0.00
> ATOM 3 2HA GLY 1 24.150 41.740 18.280 1.00 0.00
> ATOM 4 3HA GLY 1 25.220 40.740 19.300 1.00 0.00
> ATOM 5 C GLY 1 24.170 39.640 17.780 1.00 0.00
> ATOM 6 O GLY 1 24.490 39.140 16.700 1.00 0.00
> .
> .
> .
> ATOM 1035 N GLY 60 35.450 46.770 38.960 1.00 0.00
> ATOM 1036 H GLY 60 35.810 46.010 38.390 1.00 0.00
> ATOM 1037 CA GLY 60 36.430 47.230 39.920 1.00 0.00
> ATOM 1038 2HA GLY 60 35.990 47.260 40.920 1.00 0.00
> ATOM 1039 3HA GLY 60 36.850 48.200 39.670 1.00 0.00
> ATOM 1040 C GLY 60 37.680 46.390 40.110 1.00 0.00
> ATOM 1041 O GLY 60 37.810 45.380 39.370 1.00 0.00
>
> after loadpdb file:
>
> Added missing heavy atom: .R<CGLY 60>.A<OXT 8>
> total atoms in file: 24095
> Leap added 4 missing atoms according to residue templates:
> 1 Heavy
> 3 H / lone pairs
>
> thus, 24099 atoms should be in .prmtop and .inpcrd files. is it true?
>
> and after saveamberparm:
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 359 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CGLY 1
> NGLY 1
> WAT 7406
> )
> (no restraints)
>
>
> is there problem?
>
> when I visualize my generated .prmtop and .inpcrd files by VMD, it differs
> from initial pdb file (there are
> undesirable bonds between atoms)
>
> how to fix it?
> _______________________________________________
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> 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 Sat Dec 11 2010 - 11:00:02 PST
