[AMBER] problem with parametrization of an organo-metallic cluster using RED server

From: <moitrayee.mbu.iisc.ernet.in>
Date: Thu, 17 Feb 2011 13:48:13 +0530 (IST)

Dear Users,

I am trying to get the FF for an organo-metallic moiety
using RED server. I have successfully generated the p2n
files using Ante_R.E.D. 2.0 and visualized the output in
VMD. Things look alright.

However, when I submitted this p2n file for a geometry
optimization using R.E.D. IV on the server (mode 1),
I get the following error.

          Checking before running a R.E.D. Server/R.E.D. IV job


The maximum number of atoms for a molecule/conformation in a P2N input file
handled by R.E.D. Server/R.E.D. IV is set to 150 atoms.
For the reasons of this choice read http://q4md-forcefieldtools.org/REDS/faq.php#16

No problem to report in this R.E.D. Server/Ante_R.E.D. IV job. Let's start the
job...


                      ---------------------------
                     * Welcome to R.E.D. Server *
                    R.E.D. Server executes R.E.D. IV
                      ---------------------------
                      * Welcome to R.E.D. IV *
                         RESP ESP charge Derive
                  http://q4md-forcefieldtools.org/RED/

                        CHARGE MODEL = RESP-A1A
        Charge model RESP-A1A is compatible with the Cornell et al. force field.
                      ---------------------------
                  Date: jeu fév 17 09:06:09 CET 2011
                  Machine: node21.q4md-forcefieldtools.org
                      ---------------------------
                  Number of cpu(s) used in the QM job(s): 8
                      ---------------------------

                        * Operating system *
Linux node21.q4md-forcefieldtools.org 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3
16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux

                 The all atom force field library model has been selected !

        DID YOU PREPARE YOUR P2N INPUT FILES USING ANTE_R.E.D. 2.0/R.E.D SERVER?
        WE STRONGLY RECOMMAND YOU TO USE ANTE_R.E.D. 2.0/R.E.D SERVER TO PREPARE YOUR
P2N FILES...

  ===========================================================================
  ======================= Single molecule ===========================
         The molecule TITLE is "MOLECULE"
                The TOTAL CHARGE value of the molecule is "0"
              The SPIN MULTIPLICITY value of the molecule is "1"
  ===========================================================================

                     * 1 conformation(s) selected *

                               WARNING:
                  A 2nd column of atom names is detected
   This 2nd column will be used in the generation of the PDB & Tripos files

            * Selected three atom based re-orientation(s) *
                         2 re-orientation(s):
                            1 5 7
                            7 5 1

                        * Selected QM Software *
                                G09

                         * Software checking *

                               WARNING:
    Gaussian outputs generated by R.E.D. Server are stripped by R.E.D. IV
                    (in agreement with Gaussian Inc.)
         Only pieces of information related to charge derivation
                 are conserved in the Gaussian outputs.

           g09 [ OK ]
           resp [ OK ]


           The Scratch directory defined for Gaussian is
/tmp/R.E.D.IV-11394.master0.q4md-forcefieldtools.org

           Scratch directory for Gaussian [ OK ]


   Geometry optimization(s) is/are being computed for molecule 1 ... [ FAILED ]
        See the file(s) "JOB1-gau_m1-1.out"



                Execution time: 0 h 0 m 0 s

 *************************************************************************
  R.E.D. I was developed at the "Faculte de Pharmacie" in Amiens by:
           A.Pigache,(1) P.Cieplak(2) & F.-Y.Dupradeau(1)

  R.E.D. II was developed in D.A.Case's laboratory at "TSRI" by:
         T.Zaffran,(1,3) P.Cieplak(2) & F.-Y.Dupradeau(1,3)

  R.E.D. III developments were initiated in D.A.Case's laboratory at TSRI
        & are now carried out at the "UFR de Pharmacie" in Amiens by:
      E.Garcia,(5) N.Grivel,(1,3) P.Cieplak(4) & F.-Y.Dupradeau(1,3,5)

  R.E.D. IV is developed at the "UFR de Pharmacie" in Amiens by:
  W.Rozanski,(5) E.Garcia,(5) D.Lelong,(5) P.Cieplak(4) & F.-Y.Dupradeau(5)

  (1) DMAG EA 3901, Faculte de Pharmacie, Amiens, France
  (2) Accelrys Inc., San Diego, USA
  (3) D.A. Case's lab., The Scripps Research Institute, La Jolla, CA, USA
  (4) Sanford-Burnham Institute for Medical Research, La Jolla, CA, USA
  (5) CNRS UMR 6219, UFR de Pharmacie, Amiens, France
 *************************************************************************
  Do you need a new feature which is not yet available in R.E.D. Server ?
    Did you find a problem/bug in the data generated by R.E.D. Server ?
              Contact the q4md force field tools team .
                  contact.q4md-forcefieldtools.org
                               ----
               Do you need help about R.E.D. Server ?
 * Read the FAQ available at the R.E.D. Server home page.
 * Read the tutorials available . http://q4md-forcefieldtools.org/Tutorial
 - To get a general & public help, use the q4md-forcefieldtools.org
          mailing list . http://lists.q4md-forcefieldtools.org/
 - To get a private assistance, use the "Assistance" service available
          . the R.E.D. Server home page.
                               ----
       Please, submit your force field library(ies) in R.E.DD.B. at
                http://q4md-forcefieldtools.org/REDDB/
       to freely share your results within the scientific community.
 *************************************************************************

I have also attached my p2n file with this email.

It would be of immense help if someone can suggest me what to do.

Thanks a lot in advance.

Best Regards,
Moitrayee


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Received on Thu Feb 17 2011 - 08:30:04 PST
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