Re: [AMBER] Can anyone suggest me solution

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Thu, 3 Feb 2011 09:17:35 +0530

Hi Jason,
As you mentioned about the force field, I have a query regarding the same.
How can I enlist all available force fields in my installed Amber10 version.
And for modeled protein (containing a long loop region predicted by
ab-initio calculations), which forcefield would be better to proceed
further.

Hirdesh
On Thu, Feb 3, 2011 at 3:37 AM, Jason Swails <jason.swails.gmail.com> wrote:

> If you don't load a force field (i.e. source leaprc.ff99SB), then as soon
> as
> you load the PDB you're hit with similar messages. However, Bill is right:
> the FATAL messages will only appear after a failed "saveamberparm', which
> means that *some* force field parameters were loaded. However, these lines
> (along with many others) are worrisome
>
> FATAL: Atom .R<CYS 2510>.A<C 3> does not have a type.
> FATAL: Atom .R<CYS 2510>.A<O 4> does not have a type.
>
> CYS is a standard residue in every force field, and C and O are standard
> atomic names in the current and previous recent PDB standards. As such, I
> have to conclude that no *correct* force field was loaded. Perhaps the
> user
> initially just loaded their frcmod that they created for a custom residue
> but not any full force field (i.e. leaprc.ff99SB). I think this reproduces
> that error.
>
> It could also be a case of corrupted template files, I'm really not sure.
> Not quite enough information was given to debug this issue.
>
> All the best,
> Jason
>
> On Wed, Feb 2, 2011 at 3:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > That would have the symptom of missing parameters, not missing types.
> >
> > > or, as Jason said, in inappropriate force field selected (or not
> > > selected at all)..
> > >
> > > On Wed, Feb 2, 2011 at 10:59 PM, Dmitry Nilov <nilovdm.gmail.com>
> wrote:
> > > > It seems that your problem results from incorrect atom names in input
> > > > pdb (is it pdb?) file.
> >
> >
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Wed Feb 02 2011 - 20:00:02 PST
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