AMBER Archive (2009)

Subject: Re: [AMBER] trouble using iAPBS

From: Oliver Kuhn (oak.amber_at_web.de)
Date: Thu Oct 01 2009 - 06:31:51 CDT

> 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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