Hi Eliana –

 

That’s odd.  Can you send the offending PDB file?

 

Thanks,

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997

http://nabaker.me

 

From: Eliana Asciutto [mailto:ekasciut@gmail.com]
Sent: Tuesday, October 02, 2012 6:59 AM
To: apbs-users@googlegroups.com
Subject: [apbs-users] capped peptide

 


Hi all,

When trying to generate pqr for a capped peptide with charmm or amber force field through the server, the code doesn't recognize the atoms in the term residues and deletes them.

Checking for missing heavy atoms... 
        Missing OXT in ALA A 7
        Extra atom NT in ALA A 7! - Deleted this atom.
        Extra atom HNT in ALA A 7! - Deleted this atom.
        Extra atom CAT in ALA A 7! - Deleted this atom.
        Extra atom HT1 in ALA A 7! - Deleted this atom.
        Extra atom HT2 in ALA A 7! - Deleted this atom.
        Extra atom HT3 in ALA A 7! - Deleted this atom.


Since I have also ions in the pdb I need to use charmm or amber in order to have the ions read properly. Any suggestion?

Thanks!

Eliana
.