The choice of the force field actually depends on your task. ff99SB is
very effective for protein simulations that was approved in a number
of articles.
On Thu, Feb 3, 2011 at 6:47 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> 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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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Feb 02 2011 - 22:30:05 PST
