Yes, it looks that something is wrong with data in PQR file (see below):
We use it to assign protonation stage at given pH value (8.5). But it
creates PQR output, not PDB.
OK, I'll try to fix problem. Thanks!
REMARK 1 PQR file generated by PDB2PQR (Version 1.7)
REMARK 1
REMARK 1 Forcefield Used: amber
REMARK 1 Naming Scheme Used: amber
REMARK 1
REMARK 1 pKas calculated by propka and assigned using pH 8.50
REMARK 1
REMARK 5 WARNING: Propka determined the following residues to be
REMARK 5 in a protonation state not supported by the
REMARK 5 amber forcefield!
REMARK 5 All were reset to their standard pH 7.0 state.
REMARK 5
REMARK 5 N-terminal N+ 43 A (neutral)
REMARK 5
REMARK 5
REMARK 6 Total charge on this protein: -5.0000 e
REMARK 6
ATOM 1 N GLY A 43 15.790 10.898 22.016 0.2943 1.8240
ATOM 2 CA GLY A 43 15.226 9.598 22.436 -0.0100 1.9080
ATOM 3 C GLY A 43 16.346 8.666 22.835 0.6163 1.9080
ATOM 4 O GLY A 43 17.442 9.129 23.131 -0.5722 1.6612
ATOM 5 H2 GLY A 43 15.526 11.601 22.676 0.1642 0.6000
ATOM 6 H1 GLY A 43 16.787 10.828 21.979 0.1642 0.6000
ATOM 7 H3 GLY A 43 15.435 11.134 21.112 0.1642 0.6000
ATOM 8 HA2 GLY A 43 14.611 9.746 23.211 0.0895 1.1000
ATOM 9 HA3 GLY A 43 14.710 9.207 21.674 0.0895 1.1000
ATOM 10 N SER A 44 16.086 7.375 22.720 -0.4157 1.8240
ATOM 11 CA SER A 44 17.013 6.330 23.102 -0.0249 1.9080
ATOM 12 C SER A 44 17.433 5.547 21.868 0.5973 1.9080
ATOM 13 O SER A 44 16.611 5.320 20.974 -0.5679 1.6612
ATOM 14 CB SER A 44 16.337 5.382 24.057 0.2117 1.9080
ATOM 15 OG SER A 44 17.122 4.222 24.244 -0.6546 1.7210
On Thu, Jun 9, 2011 at 4:36 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jun 09, 2011, Azat Mukhametov wrote:
>
> > I use another computer for calculations, just checked:
> > I used:
> > prot = loadpdb prot.pqr
> > It gives huge number of warnings and mistakes
>
> Can you look carefully at the first few error messages, and/or post the
> beginning of your pqr file? A wild guess is that PDB2PQR is putting out an
> odd format, not really compatible with pdb, or perhaps with the Amber
> libraries.
>
> I'm not sure I understand the original problem: why not use the pdb file
> that
> you used for input to PDB2PQR? Or is there some other reason you have a
> pqr
> format file, but not a pdb format file?
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 09 2011 - 03:30:02 PDT
