Hi Bill,
Thank you so much. That's the right information I was looking for!!
Best regards,
Seungyeul
On May 18, 2010, at 6:44 PM, Bill Miller III wrote:
> 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
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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>
>
>
> --
> 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 - 16:00:06 PDT
