AMBER Archive (2004)

Subject: RE: AMBER: (no subject)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 13 2004 - 12:32:22 CDT

Dear Anshul,

The Plastocyanin tutorial gives details of how to create your own resiude
and using in leap with a protein:
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial.html

However, this assumes that you have suitable parameters for this residue. If
you currently don't have parameters then there are a number of ways you can
proceed:

1) You can allocate atoms types for your non-standard residue based on
analogy with the atom types available in the force field you have chosen to
use for your protein. You may still have some missing parameters that you
will need to resolve yourself.

2) You can check the literature and see if anyone has published parameters
for your residue and then adapt them to your needs.

3) You can go about deriving your own parameters based on QM calculations
and experimental data. This is very time consuming but should give you the
best results in the long run.

4) You could use the GAFF force field for your non-standard residue and then
use Antechamber to assign the atom types for you. You should be able to
combine the GAFF force field (designed for small molecules) with the more
specialised amino acid force fields (like ff99) but be aware of exactly what
you are doing and what the implications are.

I would start by going through the Plastocyanin tutorial.

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 |

> I have generated resp charges for my system using RED (GAMESS and QM
> software). Now I want to proceed to generate its paameters so
> that I can
> use it in sander. I want to atach it to a protein molecule and then do
> minimzation and dynamics.
> can anyone tell me how to proceed now from the resp charges?
>
> thanks in advance for all the valuable suggestions and advises.
> with regards
>
> Anshul Awasthi
> Bioinformatics Center
> Institute of Microbial Technology
> Chandigarh, India.
> Mobile +91-9872220352
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu