AMBER Archive (2004)

Subject: AMBER: Problem with computing Resp charges using RED

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Dec 25 2004 - 09:54:54 CST

Dear amber members,

I have been recently working on preparing a prep file
for a glucose derivative which I finally plan to use
it as a residue in the glycam04 library.

I already have GAMESS and RED running on my computer.

The glucose derivative has two positive charges.
In order to use the glucose derivative as a residue, I
removed the alpha OH group to set the anomeric C1 as
tail and saved the unit in pdb format in tleap. I then
generated bond connections in the pdb file using
babel. I also added reorientation iformation
in the pdb file.

I set parameters in RED.pl as follows:

$XRED = "OFF";
$QMSOFT = "GAMESS";

$OPT_Calc = "ON";
$MEPCHR_Calc = "ON";

$CHR_TYP = "RESP";
$CHR_VAL = "2";

$TITLE = "DAG";
$DIR = "/home/jenk/dag";
$MOL_START = "./dag.pdb";
$JOB_OPT = "./JOB1.log";

I ran RED to process the pdb file and I got
an error message regarding MULT.

Here is the error message at the end of JOB1-gam.log:

*** CHECK YOUR INPUT CHARGE AND MULTIPLICITY ***
 THERE ARE 87 ELECTRONS, WITH CHARGE ICHARG= 2
 BUT YOU SELECTED MULTIPLICITY MULT= 1
 EXECUTION OF GAMESS TERMINATED -ABNORMALLY-
 AT Sat Dec 25 16:50:38 2004
 100000 WORDS OF DYNAMIC MEMORY USED
 STEP CPU TIME = 0.03
 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
 TOTAL WALL CLOCK TIME= 0.0 SECONDS,
 CPU UTILIZATION IS 100.00%
 A fatal error occurr on DDI Process 0.
 ddikick.x: application process 0 quit unexpectedly.
 ddikick.x: Sending kill signal to DDI processes.
 ddikick.x: Execution terminated due to error(s).

  

Now, RED seems to be OK with all necessary software
such as rungms, gamess.01.x,ddikick.x and resp.
I think that the missing OH group could be the
problem. In other words, default RED.pl settings for
GAMESS may not be suitable for units with missing
valencies.

Here is the gamess input paramters that I pasted
from JOB1-gam.inp

$CONTRL ICHARG=2 MPLEVL=0 EXETYP=RUN
          SCFTYP=UHF MAXIT=200 RUNTYP=OPTIMIZE
          MULT=1 UNITS=ANGS INTTYP=HONDO
          QMTTOL=1.0E-08 ITOL=30 ICUT=20
          COORD=UNIQUE $END
 $SCF CONV=1.0E-08 FDIFF=.F. $END
 $SYSTEM TIMLIM=50000 MWORDS=8 MEMDDI=0 $END
 $STATPT NSTEP=200 OPTTOL=1.0E-06 $END
 $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=0
          DIFFSP=.F. $END
 $GUESS GUESS=HUCKEL $END
 $DATA

I will appreciate it if anyone out there can let me
know how to optimize the GAMESS parametes above so
that I can determine charges for my glucose derivative
unit.

If it is not possible to compute resp charges for
molecules with missing valencies using RED, could
someone please let know how to prepare a prep file for
new residues (with a missing valency) without
disturbing the charge integers?

regards,

jenk
 

                
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