AMBER Archive (2007)

Subject: Re: AMBER: tleap crashing

From: Ranjib Dey (d.ranjib_at_gmail.com)
Date: Wed Dec 12 2007 - 01:04:55 CST

hi David,
Thanks very much for ur reply..
    the problem was due to setting up disulphide bond in initial pdb file,
which i did previously.

This was solved by-
savepdb using amber and load the same file and model disulfide bond again.

thanks very much again.

-----------------------------------------------------------------------------------------------------------------
On Dec 12, 2007 4:34 AM, David A. Case <case_at_scripps.edu> wrote:

> On Wed, Dec 12, 2007, Ranjib Dey wrote:
>
> > I trying to simulate a carbohydrate-protein complex using
> glycam06/ff94
> > but , while saving *.prmtop and *.inpcrd files, tleap shows FATAL error
> and
> > crashes, although "loadpdb" and "check" is not throwing any error.
> > I am attaching the error message as well as the pdb file.
>
> Unfortunately, we need more than just the pdb file to reproduce the error,
> and hence to try to help. Can you provide a minimum set of commands, and
> all
> the files you have loaded? Note that no one on the list is likely to have
> access to glycam06.
>
> [You can also anticipate getting e-mails saying "don't use ff94 anymore!",
> but
> that is more a scientific issue than a likely cause of the crash.]
>
> You could try to simplify the pdb file to narrow down the problem. Or,
> look
> look at atoms 99 and 1914 (use savepdb to get a pdb file with the Amber
> numbering and all of the hydrogens):
>
> > !FATAL: Message: 1-4: cannot add bond 99 1914
>
> Are those atoms supposed to be bonded together?
>
> ...dac
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