Dear Dan;
Say I want to calculate both GBSA and PBSA calculations on these filtered
frames. How the script should be and how can I know which is starting frame
and which is end frame?
Below a prototype script to run parallel PBSA and GBSA. How can I know
frame numbers that will be filtered?
Input file for running PB and GB
&general
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
On Mon, Jun 23, 2014 at 4:07 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Dan;
>
> Thank you so much for pointing it out. And yes we are looking at
> filtering.Lets see what comes up in binding free.
>
> Thank you again very much.
>
>
>
> On Mon, Jun 23, 2014 at 3:58 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> Hi,
>>
>> What you are talking about doing isn't really clustering per se; it's more
>> like filtering/binning.
>>
>> On Mon, Jun 23, 2014 at 7:51 AM, Soumendranath Bhakat <
>> bhakatsoumendranath.gmail.com> wrote:
>>
>> >
>> > trajin *md1.mdcrd*
>> > rms R1 first :1-198 .CA
>> > outtraj frames_rms1_md1.mdcrd maxmin R1 min 0.0 max 1.0
>> >
>>
>> This will work in older versions of CPPTRAJ; in the latest version (14)
>> this functionality has been separated from outtraj and is now the 'filter'
>> action:
>>
>> trajin md1.mdcrd
>> rms R1 first :1-198.CA
>> filter R1 min 0.0 max 1.0
>> trajout frames_rms1_md1.mdcrd
>>
>> Note there is no space between ':1-198' and '.CA'; masks should have no
>> spaces in them unless they are enclosed in quotes.
>>
>>
>> >
>> > Please suggest if this script looks good for this process. And any way
>> to
>> > calculated binding free energy on these extracted frames.
>> >
>>
>> You could probably use an MMPBSA-type approach to do this, assuming you
>> still have enough frames to get good statistics.
>>
>> Hope this helps,
>>
>> -Dan
>>
>>
>> >
>> > Help and suggestion regarding this will be highly appreciated.
>> >
>> > --
>> > Thanks & Regards;
>> > Soumendranath Bhakat
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
>
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 23 2014 - 08:00:03 PDT
