AMBER Archive (2008)

Subject: Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Tue Apr 29 2008 - 15:56:09 CDT

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_at_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_at_paris7.jussieu.fr> wrote:
>From: Barbault Florent <florent.barbault_at_paris7.jussieu.fr>
> Subject: Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
> To: amber_at_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_at_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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