Dear all,
To avoid periodicity in my selection of frames in a trajectory, can
someone please tell me how to randomly select frames from a trajectory and
dump into a new trajectory, or equivalently, simply randomize an entire
trajectory.
The only thing I saw was the random variable in the sieve function of
cluster in ptraj, but I couldn't get it work.
Thanks in advance!
Dean
On 8/12/11 7:30 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>There is a residue list in the topology file under RESIDUE_LABEL, or if
>you are talking about the ones used by leap, then they are in
>$AMBERHOME/dat/leap/lib/amino10.lib. The protonated form if ASP is ASH,
>protonated GLU is GLH, deprotonated LYS is LYN, and deprotonated CYS is
>CYM.
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
>
>On Aug 12, 2011, at 6:47 PM, "E. Nihal Korkmaz" <enihalkorkmaz.gmail.com>
>wrote:
>
>> Dear all,
>>
>> How can i find the residue list? I mean, different versions (according
>>to
>> protonation state) of Lys, Asp, Glu and Cys. I know the versions of His
>>but
>> i didn't come across anything for the other ionizable residues.
>>
>> Best,
>>
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone: 608-265-3644
>> Email: korkmaz.wisc.edu
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>
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Received on Sat Aug 13 2011 - 17:30:03 PDT
