> 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).
Note that leap, building from scratch, would have the Na's before the
waters; this may even happen if you loadpdb with a pdb in the order
above and saveamberparm, because amber puts the waters at the end
for numerical optimization of nonbonded calcs. You can use ambpdb on
your prmtop+inpcrd to see if what the order is in the generated pdb.
This would require you to reorder the coordinates in your gromacs
trajectory if they have Na after water and if your analysis focuses
on water or ions.
> 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>
Note this indicates that your terminal residue had an atom added.
Assuming this wasn't in your original trajectory, it will mess up
the analysis. The same goes for added H's:
> total atoms in file: 24095
> Leap added 4 missing atoms according to residue templates:
> 1 Heavy
> 3 H / lone pairs
The source of the OXT and maybe the H's is leap's substitution of
terminal residue types for the end residues. If you copy the leaprc
that is being loaded to the directory you are working in, you can
edit out the PdbResMap setting that directs leap to substitute N-
and C-terminal residues.
>
> thus, 24099 atoms should be in .prmtop and .inpcrd files. is it true?
I believe so.
> 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?
Not with the chain types - chain type is no longer used as far as I
know (they were only used by an obsolete analysis program), so this
msg could be omitted.
> when I visualize my generated .prmtop and .inpcrd files by VMD, it differs
> from initial pdb file (there are
> undesirable bonds between atoms)
What undesirable bonds?
Bill
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Received on Sat Dec 11 2010 - 11:30:03 PST
