AMBER Archive (2004)

Subject: AMBER: ANAL problem.

From: A.B.S.M Osman gani (osman_gani1974_at_yahoo.com)
Date: Thu Jan 29 2004 - 06:24:19 CST

Dear Amber users,

I have been using AMBER 7 on Red Hat Linux. I have done long dynamic simulations in SANDER for a ligand +Protein complex. Then trajectories were extracted with ‘ptraj’. For energy analysis, ANAL command was performed. But the anal output file shows ‘DIHEDRAL ANGLE ERROR: 1 12153 12138 12141 12147 5 0 0.0000 0.0000’

 

For your information, the command line was:

anal -O -p xwation.top -o anal.1.out -i example_anal.in -c pyrdock.1

 

example_anal.in was:

Analysis of A2 for bonding energy

   1 0 0 0 0 1

   0 0.0 0.0 0.0 0.0

   1 0 3 1 100 1

  888.0 2.0 1.2 1

   1 99.0 99.0 99.0 99.0 99.0 99.0 99.0 99.0 99.0

ENERGY

END

RECEPTOR

RES 1 255

END

SER

RES 256 256

END

END

STOP

 

RES 1-255 are the AAs of my protein and RES 256 is the ligand.

 

anal.1.out file was:

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

          Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997

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

 

 

 

   1. RESOURCE USE:

 

| New format PARM file being parsed.

| Version = 1.000 Date = 11/04/03 Time = 20:03:13

 

     Memory Use Allocated Used

     Real 4000000 503785

     Integer 800000000 435307 (static)

 

     Max Nonbonded Pairs:******** packed 1 to a machine word

 

 

   2. DATA CONTROL:

 

  Analysis of A2 for bonding energy

 

     NTX = 1 NTXO = 0 NRC = 0

     NRCX = 0 NGRPX = 70 KFORM = 1

 

     NTB = 0 BOXX = 0.000 BOXY = 0.000

     BOXZ = 0.000 BETA = 0.000

 

     NTF = 1 NTID = 0 NTN = 3

     NTNB = 1 NSNB = 100 IDIEL = 1

 

     RCUT = 888.00 SCNB = 2.00

     SCEE = 1.20 DIELC = 1.00

 

     IMAX EBMAX EANMAX EDIHMAX ENB14MAX

        1 99.00 99.00 9.00 99.00

 

     EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX

        99.00 99.00 99.00 99.00 99.00

 

 

   3. A T O M I C C O O R D I N A T E S

 

 

restrt file generated by ptraj

 

          NUMBER OF ATOMS = 27373

 

 

          loading the groups for analysis

 

    ----- END OF GROUP READ -----

 

    non-bonded pairs are generated in residue base

    and stored as residue pairs

 

    number of non-bonded residue pairs = 32244465

 

     individual pair energies greater than 99.00 kcal/mol:

 

  type groups description dist vdwnb eelnb

 

 

     individual bond energies greater than 99.00 kcal/mol:

 

   groups description rk requil dist energy

 

 

     individual angle energies greater than 99.00 kcal/mol:

 

   groups description tk tequil angle energy

    individual dihedral energies greater than 9.00 kcal/mol:

 

   groups description phase pk dihedral energy

                 1-4 Interactions: dist vdw14 eel14

 

 DIHEDRAL ANGLE ERROR: 1 12153 12138 12141 12147 5 0 0.0000 0.0000

 

What could be the problem? ANAL was ok when I did only with ligand+ water dynamics in SANDER. But it is not working for the complex.

 

Regards,

Osman Gani

Ph.D student

Department of Pharmacology

University of Tromsø

Norway

Phone: +47 776 44875

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