Hi Gokul –

 

We’ll try to look into this problem.

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: gokul vasudev [mailto:gokul472@gmail.com]
Sent: Monday, November 14, 2011 3:55 PM
To: Baker, Nathan
Cc: apbs-users@lists.sourceforge.net
Subject: Re: APBS issue

 

Respected Dr Nathan

Thanks for your response. Now I understand the Warning messages.

Actually for more clarity I am sending the input file as well as the output file.
I am unable to understand that why the output is not coming...(maybe i am doing something wrong or because i changed the grid length)

Please have a look through these files.
I really appreciate your help and support.

Thanks and regards
Gokul

On Sun, Nov 13, 2011 at 8:04 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Hello –

 

The “problems” you report with PDB2PQR are not problems.   They are warning messages about the quality of the PDB file you have submitted.

 

I don’t understand the APBS error you reported.  However, given all of the PDB2PQR issues with this PDB file, you should consider fixing the gaps and problems with the PDB file before proceeding.

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: gokul vasudev [mailto:gokul472@gmail.com]

Sent: Friday, November 11, 2011 6:45 PM
To: apbs-users@lists.sourceforge.net
Cc: Baker, Nathan

Subject: APBS issue

 

Respected Dr Nathan


Actually I am working with pdb ID: 1jv2 (My file has Chain A and Chain B only)
PDB2PQR and APBS input/output files are attached herewith this mail.

This files has some problem with both PDB2PQR and APBS.

PROBLEM WITH PDB2PQR:

1) ERROR : PDB2PQR does not recognize the the lines starting with "HETATM" in my input file (1jv2_X_Y.pdb) and gives warning (about these HETATM) in output file.(1jv2_X_Y.pqr)

2) ERROR : Gap in backbone detected between LEU A 838 and ASP A 868! (shown in 1jv2_X_Y.pqr)
    Even original pdb file has this gap.How can i handle this??

3) WARNING : Unable to debump CYS A 59 (shown in 1jv2_X_Y.pqr)
    Should i delete these type of atoms??

PROBLEM WITH APBS:
When same file is given to APBS

4) ERROR : When i give same file to APBS ,it shows this error.
   "Reading PQR-format atom data from 1jv2_X_Y.pqr.
   VASSERT: ASSERTION FAILURE!  filename vmem.c, line 245, (ram != ((void *)0))
    22483 atoms"

I don't understand this error ???
Is it co-related to errors in PDB2PQR as stated above?


Looking forward for your help and support. I apologize for so many questions.

Thanks
Gokul
Univ of Windsor