AMBER Archive (2006)

Subject: RE: AMBER: problem in saving parameter file for non-standard residue

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Fri Jan 13 2006 - 22:29:03 CST

Forgot to attach the pdb file. Here it is.

> Dear Ross,
>
> I have actually followed your tutorial five to get the parameters. I used
> the following commands:
>
> source leaprc.gaff
> loadamberprep major.resp.prepin
> loadamberparams major.frcmod
>
> Do I need to use "loadamberparams gaff.dat" in addition to "source
> leaprc.gaff" ? Also, I mentioned in my first mail that I have been able to
> create the parameter file for the non-standard residue when I don't
> include that in the actual PDB, i.e., prmtop file can be saved just for
> the non-standard residue. However, when I include that in the PDB and try
> to save the prmtop file, it gives those bond, angle and torsion problem.
> Also, my non-standard residue is a modified Serine residue. That means
> that backbone connection is same as should in the case of standard
> residues. For your reference, I am attaching a pdb file containing the
> non-standard residue with two residues each before and after that.
>
> Please clarify my doubts.
>
> Thanks,
> -Priti
>
>
>
>
>
>> Dear Priti,
>>
>> If you used antechamber to build your non-standard residue then it will
>> have
>> defined the atom types and any missing parameters based on the gaff
>> force
>> field. This force field can be used in addition to the regular FFXX
>> force
>> fields since it uses lower case atom types. In this case your parameters
>> have not been found because you did not load the gaff.dat file into
>> leap.
>>
>> Start Leap as you have been doing and then before you load your non
>> standard
>> residue and pdb etc type:
>>
>> loadamberparams gaff.dat
>>
>> You should then be able to load your non-standard residue and pdb and
>> then
>> save the prmtop file.
>>
>> Note, you may also need to load the frcmod file antechamber created if
>> necessary. You should also look at the atom types and parameters
>> antechamber
>> assigned with reference to the GAFF force field paper and make sure they
>> are
>> what you would expect...
>>
>> Note: you should probably work through the following tutorial:
>>
>> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/index.htm
>>
>> This will give you a better understanding of what Antechamber is doing.
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Department of Molecular Biology TPC15 |
>> | The Scripps Research Institute |
>> | Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>> not
>> be read every day, and should not be used for urgent or sensitive
>> issues.
>
>


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