If you search for the subroutine "create_nmode_input" in
$AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm you should be able to find the
text for the input file that is created when nmode is specified with
mm_pbsa.pl. Within this file change ntx=0 to ntx=1 in the nmode input file.
Please note that within this subroutine there is a sander minimization input
file *and *nmode input file created, so make sure to edit the correct one.
Then do a 'make clean' and 'make install' within the $AMBERHOME/src/mm_pbsa/
directory to compile the mm_pbsa.pl with these changes. Note that this
changes the source code and all subsequent runs nmode calculations will be
performed with ntx=1 unless you change it back after this calculation.
Good luck!
-Bill
On Tue, May 18, 2010 at 6:31 PM, Seungyeul Yoo <Seungyeul.Yoo.mssm.edu>wrote:
> 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 18 2010 - 16:00:05 PDT
