I've tried to rewrite this PDB file by use of Chimera, DS visualizaer or Gold-Hermes software, but these programms give the same PDB result. Which software I need to use for preparation of dataset of 50-100 compounds for Antechamber input?
Finally, I've edited this PDB file manually removing all connectivity data and all other data except those presented in
sustiva.pdb from the tutorial. But now I get the next error:
Best regards,
Andrew Voronkov,
PhD student,
Chemistry department,
Moscow State University
andrew.linux-f29d:~/MOLDYN/F2S3-6959-0308> antechamber -i 6959-0308.pdb -fi pdb -o 6959-0308.prepin -fo prepi -c b
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU, exit
Unrecognized atomic name DU0, exit
Unrecognized atomic name DU1, exit
Unrecognized atomic name DU2, exit
Unrecognized atomic name DU3, exit
Unrecognized atomic name DU4, exit
Unrecognized atomic name DU5, exit
Unrecognized atomic name DU6, exit
Unrecognized atomic name DU7, exit
Unrecognized atomic name DU8, exit
Unrecognized atomic name DU9, exit
Unrecognized atomic name DU0, exit
Unrecognized atomic name DU1, exit
05.03.09, 17:21, "Martin Peters" <martin.b.peters.me.com>:
> Hi Andrew,
> There are no coordinates in the input file (all values are zero). The
> residue name column in the pdb file may be cause of the problem.
> Also a charge of zero for this molecule seems fine to me.
> Hope this helps,
> Martin.
> Martin B. Peters, PhD
> Research Fellow
> Molecular Design Group
> School of Biochemistry & Immunology
> Trinity College Dublin, Dublin 2, Ireland
> Tel.: +353-1-8963527
> Fax: +353-1-6772400
> On Mar 5, 2009, at 1:53 PM, drugdesign wrote:
> > Dear Amber users,
> > I've got an error during use of antechamber with Divcon module. I
> > use suse 11 system 64 bit and I've installed amber with ifort-64.
> > Amber version is Amber 9.
> >
> > "Error: cannot run $AMBERHOME/exe/divcon of bcc() in charge.c
> > properly, exit", and the divcon.out file is also in attachment for
> > your consideration.
> > MAXIT can be reached because of installation problems, right? If I
> > need to change MAXIT (as posteed here http://archive.ambermd.org/200606/0019.html
> > ), which file I need to modify? How to check if net charge is
> > proper? (if to use this answer http://archive.ambermd.org/200606/0019.html)
> > .
> >
> > Best regards,
> > Andrew
> >
> > Below is divcon.out The pdb file of ligand and divcon.in are
> > attached:
> >
> > *****************************************************************************
> > * *
> > * DIVCON
> > 2005 *
> > * *
> > * Expires:
> > None *
> > ******************************************************************************
> >
> > (*) COMPILED WITH
> > DIRECTIVES:
> >
> > PLATFORM UNKNOWN
> >
> > HAS_LAPACK DEFINED
> > MPI_IS_ON
> > NOT DEFINED
> > MPI_NOMC
> > NOT DEFINED
> > CUTREPUL_IS_ON
> > NOT DEFINED
> > LARGE_MEMORY_MC
> > NOT DEFINED
> > MEMORY_OVERLAP
> > NOT DEFINED
> > SCRF_IS_ON
> > NOW ALWAYS DEFINED
> > PARAM_IS_ON
> > NOT DEFINED
> >
> > ------------------------------------------------------------------------------
> > ---------------- USER SUPPLIED KEYWORDS
> > --------------------
> > ------------------------------------------------------------------------------
> > CARTESIAN - CARTESIAN COORDINATE FORMAT SELECTED
> > AM1 - AM1 HAMILTONIAN TO BE USED
> > STANDARD - STANDARD CLOSED-SHELL CALCULATION (NO D&C)
> > DIRECT - DO NOT STORE 2-ELECTRON INTEGRALS IN SCF CALCULATIONS
> > OPT=BFGS - CARRY OUT A BFGS GEOMETRY OPTIMIZATION
> > XTEST=0.0001 - GEOMETRY OPTIMIZATION COORDINATE CHANGE CRITERION =
> > 0.00010
> > CHARGE=0 - A NET CHARGE OF 0.00 TO BE PLACED ON SYSTEM
> >
> > ------------------------------------------------------------------------------
> > ---------------- ADDITIONAL(DEFAULT) KEYWORDS
> > ------------------
> > ------------------------------------------------------------------------------
> > ECRIT=4.0E-06 - CONVERGENCE CRITERION FOR ENERGY
> > DCRIT=5.0E-04 - CONVERGENCE CRITERION FOR DMX (DENSITY MATRIX)
> > MAXIT=100 - MAXIMUM NUMBER OF SCF ITERATIONS ALLOWED
> > TEMPK=1000.0 - A D&C TEMPERATURE REQUESTED
> > ADDMM - ADD MM CORRECTION TO PEPTIDE TORSIONAL BARRIER
> > RMIN=0.5 - MIMIMUM DISTANCE ALLOWED BETWEEN ATOMS
> > INTGLS=TALMAN - TALMAN INTEGRALS TO BE USED
> > NOXML - DO NOT GENERATE AN XML FILE
> > MAXOPT=0 - MAXIMUM NUMBER OF GEOMETRY OPTIMIZATION CYCLES; IT IS
> > TEN TIMES THE NUMBER OF SOME GEOMETRICAL PARAMETERS
> > ETEST=2.0E-03 - GEOMETRY OPTIMIZATION ENERGY CHANGE CRITERION
> > GTEST=5.0E-01 - GEOMETRY OPTIMIZATION GRADIENT COMPONENT CRITERION
> > DIIS - USE DIIS METHOD IN BFGS GEOMETRY OPTIMIZATION
> > ------------------------------------------------------------------------------
> > NPAIRS = 1540
> >
> >
> > NUMBER OF ATOMS = 56
> > TOTAL NUMBER OF BASIS FUNCTIONS = 164
> > TOTAL NUMBER OF ELECTRONS = 180
> >
> >
> > DEFAULT SETTINGS FOR CALCULATION
> > --------------------------------
> >
> > - D&C TEMPERATURE OF 1000.00 K WILL BE USED
> > - NO TIME LIMIT ON CALCULATION
> >
> >
> > ETEST = 0.002000
> > XTEST = 0.000100
> > GNTEST = 1.620185
> > GTEST = 0.500000
> >
> > NUMBER OF VARIABLES= 168
> >
> > UPDATING PAIRLIST
> > NPAIRS = 1540
> >
> > WARNING: NO CONVERGENCE IN SCF CALCULATION; MAXIMUM ITERATION COUNT
> > (MAXIT=100) HAS BEEN REACHED
> >
> > CYCLE = 0 TIME = 2.042 ENERGY = NaN
> > GNORM = NaN GRDMAX = NaN GRDAVR = NaN
> > DELTAE = 0.000000 DELTAX = 0.000000
> >
> > WARNING: NO CONVERGENCE IN SCF CALCULATION; MAXIMUM ITERATION COUNT
> > (MAXIT=100) HAS BEEN REACHED
> > <
> > 6959
> > -0308.pdb><divcon.in>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
----- В пересылаемое сообщение вложены файлы: -----
6959-0308.pdb, sustiva.pdb
-------- Завершение пересылаемого сообщения --------
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Received on Sun Mar 08 2009 - 01:11:25 PST
