AMBER Archive (2004)

Subject: Re: AMBER: Problem with computing Resp charges using RED

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Dec 29 2004 - 14:54:05 CST

Dear Cenk Andac,

> 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.

- With R.E.D. you will _not_ generate 'prep' files but 'Tripos .mol2' files (if
the atom connectivities are available in the initial PDB file). Then, if you
have AMBER8 you can load this 'Tripos' file format (as a 'prep' file) in LEaP
to generate your new LEaP OFF library and/or your prmtop/prmcrd files.
- With R.E.D. (versions I & II) you generate RESP charges derived using a two
stage RESP fit. I am not sure people from the Woods group use such an approach
to derive RESP charges for their GLYCAM force field. You should check that. We
might add something for that in R.E.D.-III

> 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.

Does it mean you optimize a structure without the anomeric hydroxyl ?
If so, I am not surprised you get the error message below. Indeed, you must
optimize the whole sugar and derive the RESP/ESP charges with this hydroxyl.
Then (in a second step) you have to add intramolecular restraints to set the
charge of this chemical group to zero (I guess) to be able to remove it.

> 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";

Looks good here.

> 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).

Yes you 'cut' your structure, so the multiplicity is wrong...

> 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.

The problem is not with R.E.D. but with optimizing & computing the MEP for your
structure without this OH.

> 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.

Optimize the whole structure and derive RESP charges for this whole structure
and then add intra-molecular restraints for the fragment you want to remove

> 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?

Please read ALL the FAQ where you will find a lot of information
and in particular http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27
All the information you need is there...

regards, Francois

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