Hey Dulal,
As an aside, if you're trying to do cpH-MD solely to predict residue side chain pKas, I would consider pKa-ANI, which has performed similarly to cpH-MD but is way less of a headache to run. Simply run conventional MD for sufficient sampling (their paper does 50 ns, you could do GaMD for more sampling) then use their program to compute pKas on the saved frames, and plot those pKas as a histogram to find mean/median/std deviation.
https://pubs.rsc.org/en/content/articlelanding/2022/sc/d1sc05610g
https://github.com/isayevlab/pKa-ANI
Regards,
Skanda
> On Feb 20, 2024, at 10:45 PM, Dulal Mondal via AMBER <amber.ambermd.org> wrote:
>
> Not clear sir.
>
>> On Tue, 20 Feb, 2024, 11:38 pm Adrian Roitberg via AMBER, <amber.ambermd.org>
>> wrote:
>>
>> the error is clear, right ?
>>
>>
>> Error: Same pH (5.9) found twice!
>>
>>
>>
>>
>>
>>> On 2/20/24 5:16 AM, Dulal Mondal via AMBER wrote:
>>> [External Email]
>>>
>>> Dear Experts,
>>> I run the constant pH remd with 10 replicas from pH 5.5 to 6.4 with 0.1
>> pH
>>> gap. I type the following command
>>> *cphstats --fix-remd prod001 ../001/cpout.rep.001 ../002/cpout.rep.001
>>> ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
>>> ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
>>> ../009/cpout.rep.001 ../010/cpout.rep.001*
>>> But it show the following error message.
>>> Error: Same pH (5.9) found twice!
>>> Thanking You
>>> --
>>> *With regards,*
>>> *Dulal Mondal,*
>>> *Research Scholar,*
>>> *Department of Chemistry,*
>>> *IIT Kharagpur, Kharagpur 721302.*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Dr. Adrian E. Roitberg
>> V.T. and Louise Jackson Professor in Chemistry
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
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>>
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Received on Wed Feb 21 2024 - 05:00:02 PST
