AMBER Archive (2004)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Dec 30 2004 - 11:30:34 CST

Dear Francois

Thanks for your reply. I have now tested RED with
uridine blocked with acetyl and n-methyl amine groups
at the 5' and 3' ends.
RED got stuck with the guess option of minimization
process. Although the JOB1_gam.log file says
the Guess process should have taken about 1.3 minutes,
it has been about an hour and the guess process is
still waiting for something (I think!).
I am sending the last lines of the JOB1_gam.log for
you to see so that you can tell me if there is
anything wrong with the Guess process.

Best regards,

Jenk

...... END OF ONE-ELECTRON INTEGRALS ......
 STEP CPU TIME = 2.15 TOTAL
 CPU TIME = 2.3 ( 0.0 MIN)
 TOTAL WALL CLOCK TIME= 3.9 SECONDS,
 CPU UTILIZATION IS 59.22%

          -------------
          GUESS OPTIONS
          -------------
          GUESS =HUCKEL
NORB = 0 NORDER= 0
MIX = F PRTMO = F
PUNMO = F
TOLZ = 1.0E-08 TOLE = 1.0E-05
SYMDEN= F PURIFY= F

 INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.
 HUCKEL GUESS REQUIRES 1521816 WORDS.

 SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH
SET(S).
   103 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS).
31=A 32=A 33=A 34=A 35=A

36=A 37=A 38=A 39=A 40=A
41=A 42=A 43=A 44=A 45=A
46=A 47=A 48=A 49=A 50=A
51=A 52=A 53=A 54=A 55=A
56=A 57=A 58=A 59=A 60=A
61=A 62=A 63=A 64=A 65=A
66=A 67=A 68=A 69=A 70=A
71=A 72=A 73=A 74=A 75=A
76=A 77=A 78=A 79=A 80=A
81=A 82=A 83=A 84=A 85=A
86=A 87=A 88=A 89=A 90=A
91=A 92=A 93=A 94=A 95=A
96=A 97=A 98=A 99=A 100=A
101=A 102=A 103=A 104=A 105=A
106=A 107=A 108=A 109=A 110=A
111=A 112=A 113=A
 ...... END OF INITIAL ORBITAL SELECTION ......
 STEP CPU TIME = 76.69 TOTAL
 CPU TIME = 79.0 ( 1.3 MIN)
 TOTAL WALL CLOCK TIME= 111.6 SECONDS,
 CPU UTILIZATION IS 70.75%

--- FyD <fyd_at_u-picardie.fr> wrote:

> 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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