Re: AMBER: Non-standard amino acid residue

From: FyD <>
Date: Thu, 19 Jul 2007 13:26:39 +0200

Quoting Sergey Samsonov <>:

> In case $OPT_Calc ="On" I receive:

> ERROR: The Scratch directory is NOT empty

This means your QM scratch directory is not empty: this has nothing to
do with $OPT_Calc ="On" or $OPT_Calc ="Off". Just do a "rm *" in this
QM scratch directory. This means you previously run R.E.D., GAMESS or
Gaussian and a QM job did not correctly ended. Thus, you still have
temporary QM files in your QM scratch directory.

In my .cshrc the QM scratch directory is defined as follows:
setenv SCR /usr/local/0QM_SCR
setenv GAMESS_SCR /usr/local/0QM_SCR
setenv GAUSS_SCRDIR /usr/local/0QM_SCR

(The QM scratch file being also set in the "rungms" GAMESS-US script;
see "set SCR=/usr/local/0QM_SCR" at the beginning of this file (line ~
Use "chmod -R 777 /usr/local/0QM_SCR" to get the right permissions in
this directory.

I defined an alias in my .cshrc as alias RM 'rm -rf $SCR/*'.
Then, I clean up the scratch directory each time required using the RM
alias instead of the rm command.

> In case $OPT_Calc ="On" I receive:

> ERROR: The optimization OUTPUT can not be found

No, here you use $OPT_Calc ="Off"; This means you have to provide the
QM ouput (geometry optimization job obtained from a previous
standalone execution) as input for R.E.D. The file name for a QM
output is once again fixed; it follows similar rules to the P2N file;
however with the .log extension instead of the .p2n one; i.e.
Mol_red1.log etc...

> I tried both own examples and the ones from Tutorial. It seems like I
> should probably change the names of some files but I cannot understand
> which ones.

- If $OPT_Calc ="On", you only need to provide P2N file(s).

- If $OPT_Calc ="Off", you need to provide P2N file(s) with its(their)
corresponding QM geometry optimization ouput(s). In this case, for
each molecule you need to provide a couple of files:
Mol_red1.p2n/Mol_red1.log, Mol_red2.p2n/Mol_red2.log etc...

Mol_red$n.p2n/Mol_red$n.log files have to be with the
script in the same (working) directory.

regards, Francois

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Received on Sun Jul 22 2007 - 06:07:30 PDT
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