AMBER Archive (2009)

Subject: Re: [AMBER] divcon error during antechamber run, convergence problem

From: Martin Peters (martin.b.peters_at_me.com)
Date: Thu Mar 05 2009 - 08:21:19 CST

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>_______________________________________________
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