AMBER Archive (2007)

Subject: RE: AMBER: BUG? Does TLEAP understand SPC/E water?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 01 2007 - 13:23:35 CDT

Dear David,

You need to do the following:

HOH=SPC
WAT=SPC
loadamberparams frcmod.spce

See Page 29 of the Amber 9 manual.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | 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.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of David Cerutti
> Sent: Friday, June 01, 2007 10:35
> To: amber_at_scripps.edu
> Subject: AMBER: BUG? Does TLEAP understand SPC/E water?
>
> Hello,
>
> I'm now being very careful about the topology files
> generated by TLEAP
> because the results I'm getting don't match some of those reported by
> others.
>
> When I change a leaprc file to reference the SPC water in
> solvents.lib
> rather that TIP3P, by adding the following lines:
>
> HOH = SPC
> WAT = SPC
>
> rather than "HOH = TP3" / "WAT = TP3" as the default seems to
> be, it seems
> that this should direct TLEAP to look in the same
> solvents.lib file where
> it finds the TIP3P parameters and find instead the SPC/E
> parameters and
> put those in the topology wherever it finds water in the simulation.
>
> The part I'm scratching my head about is that it DOES obtain the
> correct charges (I've had to figure out what AMBER's unit
> conventions are
> in that topology file, but I've verified that generating the
> topology with
> "WAT = SPC" gives the charges I'd expect for SPC/E, and they
> are different
> that those you get with "WAT = TP3"). But, TLEAP still
> inserts the TIP3P
> parameters for Lennard Jones A and B coefficients, as well as bond
> lengths--the TIP3P OH bond length is 0.9572, and this is
> still what I see
> for the SPC/E topology, even though the OH bond length should
> be 1.0000.
>
> I found this when I was trying to convert my own PDB, a
> box of 1728
> water molecules, into a topology and coordinate files.
> However, when I
> used a "solvateBox x SPCBOX 14.0" command in another study to
> solvate a
> protein in SPC/E water, I find that I actually obtained similar
> results--the charges in the topology were correct, but the
> bond lengths
> remained those of TIP3P and the Lennard-Jones A and B
> coefficients were
> also those of TIP3P, not SPC/E.
>
> It seems that there is a major problem somewhere. Either
> I didn't know
> about some subtle, additional command that I needed to insert
> to include
> the rest of SPC/E water in the setup, in which case TLEAP
> needs to be made
> more user-friendly, or there is some bug in TLEAP that makes
> it think that
> SPC/E water has the same geometry and Lennard-Jones
> parameters as TIP3P (I
> checked the solvents.lib file, and it has the correct geometry and LJ
> parameters for both TIP3P and SPC/E).
>
> The result is the same whether I use TLEAP from Amber8 or Amber9.
>
> Please help!
>
> Dave
> --------------------------------------------------------------
> ---------
> 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