Hello Bill
I am till now not able to solve the problem
Earlier I have used following parameter:
Input file for running entropy calculations using NMode
&general
endframe=15000, keep_files=1, strip_mdcrd=0,
/
&nmode
nmstartframe=1, nmendframe=15000,
nminterval=60, nmode_igb=1, nmode_istrng=0.1,
/
and got warning Not all of your snapshots minimized within tolerable limits for
nmode. But when I changed default value of drms and maxcyc
Input file for running entropy calculations using NMode
&general
endframe=15000, keep_files=1, strip_mdcrd=0,
/
&nmode
nmstartframe=1, nmendframe=15000,
nminterval=60, nmode_igb=1, nmode_istrng=0.1, maxcyc=11000, drms=0.001
/
and again I got same warning Not all of your snapshots minimized within
tolerable limits for nmode.
> If your snapshots do not properly minimize, then they will not be included
> in the nmode calculations. You should be able to fix this by adjusting the
> convergence criteria (either tolerance or increasing the minimization
> steps) in the MMPBSA.py input until all snapshots are able to be minimized.
> The default minimization parameters will work for many, but not all
> systems, and may need to be tweaked depending on the specifics of a system.
>
> Good luck!
>
> -Bill
>
> On Fri, Jun 22, 2012 at 6:55 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello All
>>
>> I am calculating entropy of protein - DNA complex. I have four complex,
>> when I
>> ran MMPBSA first time then for two complex I got WARNINGS:
>> Not all of your snapshots minimized within tolerable limits for nmode
>> though it is giving delta entropy calculation.
>>
>> When I ran MMPBSA second time for two above complexes, for one complex I
>> didn't
>> got any warning but for second complex I got again same warning.
>>
>> I am not getting whey getting warning again for one complex, will it affect
>> calculated delta entropy during same run?
>>
>>
>> Sangita Kachhap
>> SRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> ______________________________________________________________________
>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>> पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>>
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>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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>
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 28 2012 - 02:30:03 PDT
