AMBER Archive (2009)

Subject: [AMBER] Re: Error in REDIII

From: FyD (
Date: Fri Jul 03 2009 - 09:59:30 CDT

Dear Bagheri,

> I have many question about RED program and RED server,

If your questions are general please send them in the Amber of
q4md-forcefieldtools mailing lists, so that everybody can answer/read.

> I must simulate the subtilisin by AMBER package ,the enzyme with a Ca ion.
> I read the tutorial about simulate a protein with metal ion in
> AMBER workshop, on this the author introduce RED server.
> Ca ion in the Subtilisin isn't in the active site and only has the
> structural role, I didn't Know for driving the charge of the amino
> acid near the Ca , how many conformation of this molecule that I need?

If you want to model subtilisin with Ca++ ion(s), you do not need to
compute charges for your system. You only need to pick a set of
initial Cartesian coordinates for this protein (from the protein data
bank for instance) and choose a force field in the LEaP program. You
might have to perform some editing for this PDB structure (check the
atom & residue names to see if they 100 % match these available in the
force field you are going to select: parm99SB or ff03, I guess).

> 2- I uploaded my p2n file to RED server 2 weeks ago, in MOD1
> I didn't receive second and third mails which should inform
> me about the beginning and ending the computation.
> what the problem was occur?

Yes, it seems we have a problem/bug here in R.E.D. Server... Thanks,
for reporting this problem. In this case, go directly to your Download
space/page to see if your project is available.

> 3- I also use the RED III program for driving the charge.
> first I whant to know is this program act like the red server?
> and second when I run this, I've encountered the fallowing error:
> "the optimizaton output can not be found"
> what is this error mean?

- R.E.D.-III is an interface to Gaussian/GAMESS-US/PC-GAMESS and RESP.
You download R.E.D.-III, and use it on your machine(s). This means you
need to install Gaussian, GAMESS-US or PC-GAMESS and RESP on your
machine(s) to have a working system.

- R.E.D. Server provides the last version of the R.E.D. program
(R.E.D. IV beta June 2009, so far) + Gaussian/GAMESS-US/PC-GAMESS and
RESP + a cluster to run charge derivation for new molecules and
molecular fragments.


When using R.E.D. & you get "the optimizaton output can not be found":

For each P2N file used as input in R.E.D.-III.x/R.E.D.-IV, you need to provide a log file (QM output from Gaussian, GAMESS-US or PC-GAMESS). Did you try the test cases in the R.E.D.-III.2 tools distribution ?

See also

- When $OPT_Calc = "On" & $MEP_Calc = "On" in R.E.D.-III.x/R.E.D.-IV (this correspond to the mode 1 in R.E.D. Server) you only need to provide P2N file(s).

- When $OPT_Calc = "On" & $MEP_Calc = "Off" in R.E.D.-III.x/R.E.D.-IV (this correspond to the mode 2 in R.E.D. Server) you need to provide P2N and log files.

For instance, if you want to perform a 2 molecule charge derivation, you need to provide the 4 following files if $OPT_Calc = "On" & $MEP_Calc = "Off": Mol_red1.p2n Mol_red1.log Mol_red2.p2n Mol_red2.log

On the contrary if $OPT_Calc = "On" & $MEP_Calc = "On", you only need to provide: Mol_red1.p2n Mol_red2.p2n

regards, Francois

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