Re: [AMBER] sourcing solvents.cmd quits xleap/tleap

From: Jio M <>
Date: Fri, 16 Dec 2011 05:28:19 -0800 (PST)

Dear Sir,

Thanks!!! for your reply.

I thought this is an error as this informational message (which I was considering it to be as an error) does not appear while using ff03.


 From: case <>
To: Jio M <>; AMBER Mailing List <>
Sent: Friday, December 16, 2011 6:37 PM
Subject: Re: [AMBER] sourcing solvents.cmd quits xleap/tleap
On Thu, Dec 15, 2011, Jio M wrote:
> So I just tried to loadpdb TP3.pdb having only one water (file attached
> containing one water molecule; TP3.pdb) as follows
> loadamberparams parm99.dat
> loadoff solvents.lib
> WAT = copy TP3
> p = loadpdb TP3.pdb
> I get this error
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-H1-O-*

This is not an error, just an informational message that you can ignore: TIP3P
water (as implemented in Amber) has a non-physical H-H bond, used to keep the
molecule rigid.  You can still do commands like "desc p", etc. and continue
with your work.

> source solvents.cmd
> xleap/tleap quits so I cannot loadpdb

As the message you get indicate, you can only run solvents.cmd when you are
inside the $AMBERHOME/dat/leap/lib directory.  The purpose of the solvents.cmd
file is to create solvents.lib.  Since you already have that, there is no need
to run solvents.cmd -- it's mainly there for developers, or for users who
might want to modify or extend solvents.lib.

....good luck...dac

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Received on Fri Dec 16 2011 - 05:30:03 PST
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