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From: Cenk Andac <cenk_andac.yahoo.com>

Date: Thu, 30 Dec 2004 09:30:34 -0800 (PST)

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.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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*

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*

*> To unsubscribe, send "unsubscribe amber" to
*

*> majordomo.scripps.edu
*

*>
*

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Received on Thu Dec 30 2004 - 17:53:00 PST

Date: Thu, 30 Dec 2004 09:30:34 -0800 (PST)

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.u-picardie.fr> wrote:

-----------------------------------------------------------------------

__________________________________

Do you Yahoo!?

Send holiday email and support a worthy cause. Do good.

http://celebrity.mail.yahoo.com

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Dec 30 2004 - 17:53:00 PST

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