Dear Jason;
Though ptraj seems processing the trajectory but still a warning message.
WARNING in dispatchToken: Token string "sasa.dat" not found in tokenlist
Whats the reason of that?
Best;
S.B
On Fri, May 23, 2014 at 2:29 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Thank you so much Jason. I will try both. Thank you once again.
>
>
> On Fri, May 23, 2014 at 2:16 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>>
>> On May 23, 2014, at 8:07 AM, Soumendranath Bhakat <
>> bhakatsoumendranath.gmail.com> wrote:
>>
>> > Hi All;
>> >
>> > I want to calculate SASA over time for protein-ligand complex. I have
>> > residues ranging from 1-560
>> >
>> > My cpptraj or ptraj inputs looks like that
>> >
>> > trajin md50.mdcrd
>> >
>> > surf R1 :1-560 out sasa.dat
>> >
>> >
>> > Can anyone please confirm if these SASA script looks good?
>>
>> molsurf may be a better SASA estimator than LCPO (which is used by
>> "surf"). I don't see any problems with your SASA command, but if you have
>> doubts you should run the calculation and check that the resulting values
>> make sense.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
>
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Fri May 23 2014 - 06:30:02 PDT
