Hello,
This problem happens commonly also with me. If you use a combinaison
of steepest descent followed by conjugate gradient, I suggest that you
increase the number of SD steps. Generally it works fine.
Regards
Florent Barbault
On Sat, 26 Apr 2008 17:06:13 +0530 (IST)
saurabh agrawal <imsam100.yahoo.co.in> wrote:
> Dear Amber Users,
>
> I am trying to simulate nucleotide ligand complex. But It aborted
>during the simulation once I reduce the restraints below 20 in the
>input file and gives the following error.
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 900 NaN NaN 0.0000E+00 H5T
> 1
>
>
>
> BOND = NaN ANGLE = NaN DIHED = NaN
> VDWAALS = -140.5901 EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
> EAMBER = NaN
>
>
>
>
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 1000 NaN NaN 0.0000E+00 H5T
> 1
>
>
>
> BOND = NaN ANGLE = NaN DIHED = NaN
> VDWAALS = -140.5901 EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
> EAMBER = NaN
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> The same nucleotide I have simulated with different ligands and
>those run fine. This ligand is having two Selenium atoms (which is
>not defined in the leap). Is this the reason for the problem?
>
> Every time it is stopping, and I am unable to solve it.
>
> Please help me in this regard.
>
> saurabh
>
> From Chandigarh to Chennai - find friends all over India.
> Click here.
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Received on Sun Apr 27 2008 - 06:08:12 PDT
