Hello,
Your electrostatic energy seems to be weird. Before simulate the
complex, did you try to do optimisation and MD of the ligand alone? If
these problems remain, then there is a ligand definition problem.
Regards
Florent Barbault
On Sat, 26 Apr 2008 19:45:38 +0530 (IST)
saurabh agrawal <imsam100.yahoo.co.in> wrote:
> Dear Sir,
>
> Thanks for the suggestions. On increasing the SD runs to 1800
>followed by 200 CG runs system runs fine at restraint value 20.
>
>For the same minimization run when I reduced the restraint to 10 it
>gives following output and aborts.
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 400 -1.0822E+07 1.0884E+10 1.0151E+12 Se1
> 761
>
> BOND = 2465.6712 ANGLE = 212.0772 DIHED =
> 581.1697
> VDWAALS = 3738.4993 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 208.1155 1-4 EEL = -1701.6655 RESTRAINT =
> 25.4368
> EAMBER = *************
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 500 -3.5333E+07 1.1667E+11 1.0880E+13 N1
> 783
>
> BOND = 2465.6719 ANGLE = 212.0774 DIHED =
> 581.1696
> VDWAALS = 3738.4993 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 208.1156 1-4 EEL = -1701.6655 RESTRAINT =
> 25.4369
> EAMBER = *************
>
> Please give your kind suggestion.
>
> Thanking you in advance.
>
> saurabh
>
>
>
> --- On Sat, 26/4/08, Barbault Florent
><florent.barbault.paris7.jussieu.fr> wrote:
>From: Barbault Florent <florent.barbault.paris7.jussieu.fr>
> Subject: Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
> To: amber.scripps.edu
> Date: Saturday, 26 April, 2008, 6:43 PM
>
> 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 Wed Apr 30 2008 - 06:07:55 PDT
