AMBER Archive (2005)

Subject: Re: AMBER: Question about using MM_PBSA

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Thu Nov 17 2005 - 17:50:05 CST

Hi,

You can use VMD to output pdb files for what you want. Then use leap to
generate prmtop and crd files.

Wei Chen

ÒýÓÃ gtg549i_at_mail.gatech.edu:

> Dear Amber user,
>
>
> I did a simulation annealing for a receptor-ligand complex. I need to
> calculate the interaction energy of this complex. To save computing time, i
> want to include only residues within 12 ?of the mass center of the receptor
> (excluding water molecules) for the calculation, Anyone knows how to get the
> residue numbers within 12 ?and prmtop files of the species
> (complex,receptor,
> ligand..)from the snapshots? Thanks a lot!
>
> Shuting Wei
> -----------------------------------------------------------------------
> 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