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.top FK506.crd
Checking Unit.
Building topology.
Building atom parameters.es
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
DiscoveryStudio.
#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)
#FK506.top 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 <sekijima.gsic.titech.ac.jp>:
> 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.
>
> md1.in (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.gsic.titech.ac.jp
>
SEKIJIMA Masakazu, Ph.D.
Mail: sekijima.gsic.titech.ac.jp
- application/octet-stream attachment: leap.log
- application/octet-stream attachment: FK506.top
- application/octet-stream attachment: FK506.crd
- application/octet-stream attachment: test.in
- application/octet-stream attachment: min1.in
Received on Mon Jul 06 2009 - 11:13:51 PDT
