AMBER Archive (2009)

Subject: [AMBER] Re: Error on equilibriation of Amber10

From: Masakazu SEKIJIMA (
Date: Thu Jun 25 2009 - 05:45:31 CDT

Dear amber users,

I simplified my problem and concluded that my situation was
caused by failure of GAFF usage.

But I could not determine which process was wrong.
Could someone please give me some advice for my problem?

Below comments were read out when I saved as amber parameter.
> saveamberparm FK5 FK506.crd
Checking Unit.
Building topology.
Building atom
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <FK5 1>: C2 O2 C1 O1
 <FK5 1>: C8 C6 N7 C2
 <FK5 1>: C9 N7 C8 O3
 <FK5 1>: C8 C10 C9 O4
 <FK5 1>: C20 C18 C19 C37
 <FK5 1>: C19 C21 C20 H21
 <FK5 1>: C40 C38 C39 H49
 <FK5 1>: C39 H50 C40 H51
 <FK5 1>: C21 C23 C22 O9
 <FK5 1>: C28 C42 C27 C26
 <FK5 1>: C27 C29 C28 H28
 total 11 improper torsions applied
 11 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)

brief description of attached files)
#FK506.pdb was extracted HETATOM from 1FKF.pdb and protonated by
#FK506.prepin was made by antechamber suite program.
(%antechamber -i FK506.pdb -fi pdb -o FK506.prepin -fo prepi -c bcc)
#FK506.frcmod was made by parmchk program.
(%parmchk -i FK506.prepin -f prepi -o FK506.frcmod) and FK506.crd were made by tleap and it's log is leap.log.
#FK506_min.rst and FK506_min.out were execution results by min1.csh script.
#FK506_1.out was execution failure result by test.csh script.

Best Regards,

2009/6/22 Masakazu SEKIJIMA <>:
> Dear Amber users,
> I want to simulate protein and organic molecule system.
> So, I prepared topology and coordinates files using antechamber and tleap.
> I minimized this system below input file.
> minimization
>  &cntrl
>   imin=1,
>   maxcyc=2000, cut=10.0,
>   ntpr=100, ntb=0,
>  /
> After minimization, I tried to equilibrate this system below input file.
> (10K, 1fs x 5000steps) : Initial Equilibriation
>  &cntrl
>  imin=0, nstlim=10000,
>  ntf=2, ntb=2, cut=8.0,
>  ntt=1,
>  temp0=10.0, tautp=0.2,
>  ntc=2, tol=0.00002,
>  ntp=2, taup=0.2,
>  ntpr=1000, ntwe=1000, ntwx=1000,
>  /
> But, I could not execute  equilibriation. Sander of Amber10 only
> showed below message.
>          -------------------------------------------------------
>          Amber 10 SANDER                              2008
>          -------------------------------------------------------
> I could equilibrate another system using above input file on sander of AMBER8.
> Do you have any advice on this situation?
> Best Regards,
> --
> _____
> SEKIJIMA Masakazu, Ph.D.
> Mail:

SEKIJIMA Masakazu, Ph.D.

  • application/octet-stream attachment: leap.log

  • application/x-csh attachment: min1.csh

  • application/octet-stream attachment:

  • application/octet-stream attachment: FK506.crd

  • application/x-csh attachment: test.csh

  • application/octet-stream attachment:

  • application/octet-stream attachment:

AMBER mailing list