AMBER Archive (2005)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Jan 01 2005 - 08:08:24 CST

Hi Francois,

I have found out that RED calculations take
considerable amount of hard-disk space while GAMESS is
executed. My molecule is about 300 Daltons.
I noticed that RED stopped running because my
hard-disk ran out of disk-space. RED has consumed all
my available disk space (about 2.2 GBytes!). Is this
the way RED usually works? Do I need to purchase an
extra hard-disk for RED or are there other ways to
reduce hard-disk space consumption while execution of
RED?
After excavating the GAMESS directory, I noticed that
the culprit is a bulky file (about 2.2 GByte)
generated in a temp directory of GAMESS while RED is
running.

I will appreciate your suggestions ragarding the
extreme hard-disk consumptions during execution of
RED.

regards,

jenk.
   
--- Cenk Andac <cenk_andac_at_yahoo.com> wrote:

> 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
>
=== message truncated ===

                
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