AMBER Archive (2007)

Subject: Re: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Oct 26 2007 - 12:31:03 CDT

That's correct.

Ray

On Oct 25, 2007, at 10:52 PM, Yang, Lee-Wei wrote:

> Thanks very much Ray. Very helpful. crystal waters were read in
> without problems.
> Is it saying that all-atom and united-atom forcefields in Amber
> treat TIP3 water the same way?
>
> Lee
> ________________________________________
> From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf
> Of Ray Luo [rluo_at_uci.edu]
> Sent: Thursday, October 25, 2007 2:20 PM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Including crystal water when using united-atom
> forcefield leaprc.ff03ua
>
> Lee,
>
> Before loading your pdb file, load the ion and solvent libraries
> first as
> follows:
>
> loadOff ions94.lib
> loadOff solvents.lib
> HOH = TP3
> TIP3 = TP3
> WAT = TP3
>
> All the best,
> Ray
>
>
> ==========================================
> Ray Luo, Ph.D.
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900
> Phone: (949) 824-9528
> Email: rluo_at_uci.edu
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf Of
> Yang, Lee-Wei
> Sent: Thursday, October 25, 2007 7:46 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Including crystal water when using united-atom
> forcefield
> leaprc.ff03ua
>
> Dear all,
>
> I may miss something very basic here. Is there a water model for
> united-atom
> force field such as leaprc.ff03ua?
> 'HOH' or 'WAT' in the PDB file can not be read in by leap when
> 'source
> leaprc.ff03ua'.
> I wonder how people include the crystal waters when using united
> atom force
> field in AMBER?
> (I have to use united atom force field for the deoxy-state of my
> molecule as
> suggested in
> ............./amber/amber9_patch34/dat/contrib/heme/0README)
>
> Regards,
>
> Lee
> ----------------------------------------------------------------------
> -
> 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
> ----------------------------------------------------------------------
> -
> 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