AMBER Archive (2002)

Subject: Re: Biphasic box

From: Gemma Kinsella (maynooth_at_maths.tcd.ie)
Date: Wed Dec 04 2002 - 02:15:53 CST

Hi,

Thanks for the repsonse. I did include the frcmod for CHCL3. The problem
arises because I try to add chloroform first with

solvatebox a1aa CHCL3BOX {10 10 0 }

I save the pdb prmtop and prmcrd, then add the loop bits back in and try
to read the new full pdb file (with the chloroform) back into leap and it
can't recognise them.

I can then solvate the top and bottom with water (loop,tail region)
solvatebox a1aa WATBOX216 {0 0 20 }
and save again as a pdb which looks fine in terms of the solvent
locations.

The only way I can think of doing this in one step would be
if I could use the solvate command to solvate portions of the full
protein box with different solvents. ie something like
solvatebox a1aa CHCL3BOX {10 10 -20 } (which doesn't work)
solvatebox a1aa WATBOX216 {0 0 20 }

Is there a way around this????

Thanks,

Gemma

On Tue, 3 Dec 2002, David A. Case wrote:

> On Tue, Dec 03, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
> >
> > From: Gemma Kinsella <maynooth_at_maths.tcd.ie>
> >
> > FATAL: Atom .R<CL3 355>.A<H1 1> does not have a type.
> > FATAL: Atom .R<CL3 355>.A<C1 2> does not have a type.
> > FATAL: Atom .R<CL3 355>.A<CL1 3> does not have a type.
> > FATAL: Atom .R<CL3 355>.A<CL2 4> does not have a type.
> > FATAL: Atom .R<CL3 355>.A<CL3 5> does not have a type.
>
> Have you given the "loadAmberParams frcmod.chcl3" command to LEaP?
This
> is needed to have LEaP know about chloroform parameters.
>
> ..hope this helps...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>