Hi,
I tried to do the minimization using xmin of my system.. I just changed the
*ncyc* option with *ntmin=3* in the script for xmin consideration.
But this time, the minimization starts (the mdout information is there for
NSTEP 1)
The mdout file is given below:
*NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.8644E+05 0.0000E+00 3.7844E+02 C 590
BOND = 42121.5300 ANGLE = 1131.4977 DIHED =
3216.1788
VDWAALS = 96652.4918 EEL = -744969.5912 HBOND =
0.0000
1-4 VDW = 1519.7911 1-4 EEL = 13886.2290 RESTRAINT =
0.0000*
But then it didnt proceed further and also no error is displayed....
I used following script for minimization
*Minimization of the entire molecular system
&cntrl
imin=1,ntmin=3, maxcyc=2000, cut=10.0,
ntpr=100,
&end*
Please tell me where I am wrong..
Thanks,
Hirdesh
On Fri, Jan 21, 2011 at 9:48 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Hi,
> Thanks Jason for your reply. No there was nothing written like Stderr in
> the output file.. Even there is no warning as well in mdout file. It just
> have minimization information upto steepest descent method.
>
> Hirdesh
>
>
> On Thu, Jan 20, 2011 at 7:20 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Thu, Jan 20, 2011 at 12:58 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
>> >wrote:
>>
>> > Hi Amber Users,
>> > I am doing MD of my protein bound with ligand and cofactor. The complex
>> was
>> > prepared well using antechamber and tleap modules (did not show any
>> > error).*TIP3P
>> > * water type was used to solvate the system. I minimized the protein
>> > complex
>> > (*total :5320 atoms*) using steepest descent and conjugate gradient
>> method
>> > (
>> > *Total: 2500 and ncyc:1500*). It showed "Linmin Error" when it moved
>> from
>> > steepest descent to conjugate gradient. I searched for the error and
>> found
>> > it to be related to some coordinate overlap. To solve the problem, I
>> >
>>
>> This does not seem right to me (although maybe that can cause it to
>> happen...) LINMIN failures simply imply that the minimizer got stuck and
>> couldn't figure out how to find its way "downhill". If you've hit this
>> point in the minimization, then you are typically fine to start MD if
>> that's
>> what you're aiming for. If you're really trying to find a *good* minimum,
>> then consider using the xmin minimizer (see the Amber manual, specifically
>> setting ntmin=3). Here's a page with more information
>> http://ambermd.org/Questions/linmin.html .
>>
>>
>> > optimize my complex using Schrodinger and again prepare the protein
>> complex
>> > using tleap. This time it is not showing such error (no warning in the
>> > mdout
>> > file) but still the job was killed at 1500 step. In mdout file also it
>> is
>> > not showing any warning.
>> >
>>
>> Was anything written to stderr?
>>
>> Good luck!
>> Jason
>>
>>
>> >
>> > I am confused whether I should ignore this and optimize my system using
>> > increased number of steepest descent minimization and no conjugate
>> gradient
>> > steps? Suggest me what should I do?
>> >
>> > Thanks,
>> > Hirdesh
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>
--
##################################
Hirdesh Kumar
PhD Scholar
School of Biological Sciences, IITD
(http://www.iitd.ac.in/bioschool.html)
####################################
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Received on Fri Jan 21 2011 - 01:30:02 PST
