AMBER Archive (2009)

Subject: Re: [AMBER] trouble using iAPBS

From: Robert Konecny (rok_at_ucsd.edu)
Date: Thu Oct 01 2009 - 12:27:42 CDT

Hi Oliver,

thanks for your report - you are really pushing iAPBS to its current limits
:). That's good.

Anyway, the current iAPBS version considers only ATOM records in your
supplied pqr file, it discards HETATM records. A simple fix to get you
going is to replace 'HETATM' with 'ATOM' in your pqr file.

I'll get this fixed permanently in the iapbs SVN tree.

Thanks again - and please let me know if you have any other issues.

Robert

On Thu, Oct 01, 2009 at 01:31:51PM +0200, Oliver Kuhn wrote:
> > Yes, you just need a single set of .pqr files (for lig, rec and com). iAPBS
> > uses only charge and radius values from the .pqr files and these remain
> > same for all snapshots. The actual coordinates are taken from individual
> > crd snapshots.
> > Best,
> > Robert
>
> Thank you.
> I'm still having problems getting iAPBS running.
> My ligand ist saquinavir, all heteroatoms.
> I had used am1 charges and have used the prep file to get the simulation input.
> Now, I needed a mol2 file for pdb2pqr, wrote a mol2 with leap and converted the atom types into sybyl format.
> (I had to create a new mol2 with leap, because leap had protonated the receptor.)
> Fine so far.
>
> Problem now is:
> ...
> | MDOUT: iapbs_com.1.out
> |INPCRD: ./snapshots/snap_com.crd.1
> | PARM: ./com.top
> ...
> iAPBS: Initializing APBS interface
> iAPBS: Reading charge/radii definition from pqr filename: pqr
> Wrong number of atoms in PQR file!
>
> I have attached the iapbs outfile - I'm quite sure that the number of atoms is right .
>
> tail of com.pqr:
> ...
> HETATM 3219 C11 LIG 1 14.966 -5.835 7.393 -0.0747 1.7000
> HETATM 3220 H044 LIG 1 14.555 -4.944 7.587 0.1516 1.0000
> HETATM 3221 C12 LIG 1 16.297 -5.929 6.995 0.0720 1.7000
> HETATM 3222 N3 LIG 1 17.031 -4.817 6.879 -0.4001 1.5000
>
> head of com.top:
> %VERSION VERSION_STAMP = V0001.000 DATE = 07/27/09 16:15:41
> %FLAG TITLE
> %FORMAT(20a4)
>
> %FLAG POINTERS
> %FORMAT(10I8)
> 3222 14 1659 1593 3786 2163 7132 5045 0 0
> 17932 199 1593 2163 5045 62 140 63 43 0
> 0 0 0 0 0 0 0 0 99 0
> 0
> %FLAG ATOM_NAME
> %FORMAT(20a4)
> N H2 H3 CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA
> CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB CG1
> ...
>
>
> head of snap_com.crd.1:
> 3222
> 49.2260000 40.0960000 54.4210000 49.9260000 39.6450000 53.8490000
> 48.5320000 40.2940000 53.7140000 49.7740000 41.3130000 55.0360000
> ...
>
> Maybe I'm just overlooking something, but I have no idea.
>
> Thanks for help.
> Oliver
>
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