Re: AMBER: running_RED-III

From: FyD <>
Date: Thu, 19 Jul 2007 03:33:20 +0200

Quoting Karol Kaszuba <>:

> I have a couple of questions related to RED-III execution:
> 1) I have installed resp, gamess(the newest one) and RED-III.

So you have the ddickick.x, rungms and gamess.00.x (or gamess.$n.x
with $n = 00 up to 09) binaries installed in your system.

If your system is a PC, you might also consider using PC-GAMESS since
it seems to be really faster (2 times ?). PC-GAMESS can now be
interfaced by RED-III. PC-GAMESS is used by RED-III only if at least
one of the three GAMES-US binaries is missing. Thus, on our machines,
we have GAMESS-US installed in /usr/local/gamess and PC-GAMESS in
/usr/local/pcgamess. To use PC-GAMESS I simply remove
/usr/local/gamess from my $PATH, and add it again if I want to use it
instead of PC-GAMESS (/usr/local/pcgamess being always in my $PATH).

> I checked resp and gamess - I put them in my path, I tested them (I am
> using BASH shell)- they work.
> In the RED-II manual it is wrote that I have to modify the
> ".cshrc" file
> to "run GAMESS, and "RESP program.

R.E.D. checks for binaries using the "which" UNIX command. If the
answer to "which resp" is correct, it should be OK. Same rule for the
three GAMESS-US binaries.

> First question - I am not using .cshrc so I don't have to modify .cshrc
> to run these programs under RED-III ?

You have to modify your .cshrc file _if_ you use the csh or tcsh
shell. Modify the corresponding file for BASH shell.

> 2) I modifed three lines in rungms as it is recommended in RED-II manual
> to:
> setenv IRCDATA $SCR/$JOB.irc
> setenv INPUT $SCR/$JOB.F05
> setenv PUNCH $SCR/$JOB.dat.


> 3) I used Ante_RED for p2n file generation - I checked the Ante_RED.log -
> without any errors, I edited p2n file as it is recommended in RED-III
> tutorial.

There is a bug in Ante-RED: See the 1st bugfix from the RED home page.

Yes, check in particular:
(i) the atom connectivities which might be a little particular if:
- your starting structure is bad
- you have a metal in your system
(ii) the two columns of atom names
- to select the equivalencing procedure you wish to apply during the
fitting procedure (different choices might be made depending on the
case you study)
- to select the atom names that will be available in the force field
library to the Tripos mol2 file format (two atoms cannot have two
identical atom names).

> 4) I executed (as it is recommended in RED-III tutorial) and I
> noticed an error:
> "DO NOT RUN THIS SCRIPT AS ROOT" so I modified the script -
> I deleted lines:
> if($< == 0){ print "\n\t\tERROR: DO NOT RUN THIS SCRIPT AS
> ROOT!\n\n";
> if($XRED eq "ON"){ print "\t\tPress Enter to exit.\n\n"; <STDIN>; }
> exit(0);

Yes you can indeed, de-activate this test. However, my understanding
is that it is always a _bad_ idea to execute a program as the
super-user. Thus, I would not do that. Anyway, it is a good idea to go
in the source code and to try to remove tests since you might need to
do it in other cases...

> - and I tried again - this time "Verifications of variables" passed
> without any errors but I noticed the second error:
> "The initial P2N file can not be found".

R.E.D. needs Mol_red$n.p2n files to run... For instance:
- If $n = 1 (This is a single molecule fitting approach), you only
need to provide Mol_red1.p2n (the name being fixed)...
- If $n = 3 (This is a three molecule charge fitting approach), you
need to provide three p2n files: Mol_red1.p2n, Mol_red2.p2n and
- Now, if you provide Mol_red1.p2n, Mol_red2.p2n and Mol_red4.p2n,
R.E.D. will only use the 2 first p2n files since you have a hole in
the list of p2n files.

The P2N files and script have to be in the same (working)

> I checked everything, I read carefully RED-III tutoriall,
> RED-II manual and I didn't find any clue.

In the tutorial, the scripts have been removed from the
data available for download since (i) one has to register to get
RED-III and (ii) the tutorial data are free for download.

regards, Francois

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Received on Sun Jul 22 2007 - 06:07:21 PDT
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