VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 06 2006 - 11:33:04 CDT

Also,
the bad global exclusion count is not necessarily due to a bad psf (this
is actually quite unlikely). I'd recommend having a visual look at the
psf/pdb combo generated by autopsf to make sure all the bonds are in the
right places (things look ok when I try it), and then check that your
periodic cell is big enough, you've done enough minimization, and that
you try increasing the margin a bit -- these are all far more likely
culprits for the error you've described.
Peter

Rima Chaudhuri wrote:
> Hi,
> I am still encountering the problem of generating a psf file from the
> attached pdb.
> It gives me the following errors Although the atoms do exist in the
> pdb. Secondly, it is trying to make a bond between the C(0) N(1) in
> residue ASN:299 when it should'nt!
>
> building segment U
> reading residues from pdb file NL63.pdb
> extracted 300 residues from pdb file
> Info: generating structure...
> Info: skipping improper N-C-CA-HN at beginning of segment.
> Info: skipping conformation C-N-CA-C at beginning of segment.
> Info: skipping conformation C-CA-N-HN at beginning of segment.
> ERROR: Missing atoms for bond C(0) N(1) in residue ASN:299
> ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
> in residue ASN:299
> Info: segment complete.
>
> If I use the autopsf functionality it does not give me any errors but
> later in the simulation the system gives me 'bad exclusion count error
> due to bad initial psf file.
> Please help!
>
> Thanks
> -Rima
> University of Illinois at Chicago
> Dept. of Bioengineering
> Bioinfomatics
> PhD candidate
> rchaud5_at_uic.edu <mailto:rchaud5_at_uic.edu>
>
>
>
>
> "I can tell you fancy, I can tell you plain, you give something up for
> everything you gain. Since every pleasure's got an edge of pain. Pay
> for your ticket and don't complain" - Bob Dylan
>
> ------------------------------------------------------------------------
> Yahoo! Music Unlimited - Access over 1 million songs. Try it free.
> <http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=36035/*http://music.yahoo.com/unlimited/%20>