Thanks for reply, That's very quick. =)
It didn't work either when I didn't specify NTX and the results were
same (nmode_com.in has ntx = 0).
nmode_com.in is like followings:
--------------------------------------------
File generated by mm_pbsa.pl
&data
ntx = 0, <- this should be 1
ntrun = 1, nvect = 0,
drms = 1,
dielc = 4.0, idiel = 0,
scnb = 2.0, scee = 1.2
&end
END
--------------------------------------------
How and where should I change that value in mm_pbas.pl?
Thanks,
Best regards,
Seungyeul
On May 18, 2010, at 6:18 PM, Dwight McGee wrote:
> Hi,
>
> Remove the NTX from your mmpbsa.pl input
>
> On Tue, May 18, 2010 at 6:11 PM, Seungyeul Yoo
> <Seungyeul.Yoo.mssm.edu>wrote:
>
>> Dear Amber Users,
>>
>> I am using mm_pbsa.pl version now and have a error message during
>> normal mode analysis.
>>
>> After I generated snapshots from my MD simulations (Results are
>> stable), I could calculate PB and GB solvation energy with successful
>> energy decomposition.
>>
>> However, when I tried to calculate entropy terms, nmode input files
>> indicated "ntx = 0".
>>
>> Since my coordinate files are formated, calculation stops very
>> beginning.
>>
>> Even when I set ntx = 1 in mm_pbsa input file as following, nmode
>> input files which are automatically generated by mm_pbsa.pl still
>> have
>> ntx = 0.
>>
>> .NM
>> #
>> # Parameters for sander/nmode calculation (this section is only
>> relevant if NM = 1 above)
>> #
>> # The following parameters are passed to sander (for minimization)
>> and nmode
>> # (for entropy calculation using gasphase statistical mechanics).
>> # For further details see documentation.
>> #
>> # DIELC - (Distance-dependent) dielectric constant
>> # MAXCYC - Maximum number of cycles of minimization.
>> # DRMS - Convergence criterion for the energy gradient.
>> #
>> DIELC 4
>> MAXCYC 1000
>> DRMS 0.1
>> NTX 1
>> #
>>
>> Isn't default value of ntx for normal mode 1? I'm wondering if there
>> is a way I can make nmode input files have ntx as 1.
>>
>> Thanks in advance,
>>
>> Best regards,
>>
>> Seungyeul Yoo, Ph.D Candidate
>> Department of Structural and Chemical Biology
>> Mount Sinai School of Medicine
>> Box 1677, 1425 Madison Avenue, New York, NY 10029
>> East Building, 16th floor, Room 16-34A
>> New York, NY 10029
>> +1 (212) 6595477
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 18 2010 - 16:00:04 PDT
