AMBER Archive (2008)

Subject: Re: AMBER: ptraj - closest command

From: Ryan Pavlovicz (pavlovicz.7_at_osu.edu)
Date: Wed Oct 08 2008 - 15:49:08 CDT

I figured out my initial problem: i was using 'trajectory smoothing' when
viewing the trajectory in VMD. Because the residues essentially change
identity when they leave and then reenter the 50 water sphere, this messes
up the smoothing and therefore my visualization of the solvation. I don't
think the order in which i used the 'image' command had an effect on this,
since 'closest' automatically images the waters before the distance
calculations.

So now, what i would really like to do is figure out the residue numbers of
the waters that come within a specific radius of a mask. Can ptraj do
this? This way i could then strip all but the waters i am interested then
get better tracking of the waters of interest when viewing the trajectory in
VMD. I have previously done something similar to this with the
''atomicfluct byres" command to sort the more stable waters from the more
mobile ones. While this allows me to get the numbers of most of the waters
that i am interested in, since they are stable in the binding pocket, a few
of the more transient waters are missed.

thanks again,

-ryan

On Wed, Oct 8, 2008 at 3:50 PM, Jianyin Shao <jyshao2004_at_gmail.com> wrote:

>
>
> On Wed, Oct 8, 2008 at 11:36 AM, Ryan Pavlovicz <pavlovicz.7_at_osu.edu>wrote:
>
>> Hi. I am trying to visualize an explicitly solvated MD trajectory to
>> analyze waters in a protein active site. Since it is very difficult and
>> CPU-intensive to visualize all of the waters in the entire system, i would
>> like to strip all waters but for those that enter the binding pocket. It
>> seems that the ptraj command 'closest' more or less should do what i want.
>> I tried to keep the closest 50 waters to an atom of interest:
>>
>> closestwater 50 :15_at_SG oxygen
>>
>> Then i create a new prmtop file that has my protein in addition to 50
>> waters, but the visualization in VMD seems incorrect. While all of the
>> waters are surrounding the area of interest, many of the waters i am viewing
>> seem to be intersecting each other or coming unreasonably close to the
>> protein. Here is the entire script i am using:
>>
>> #!/bin/bash
>> ptraj in.prmtop << EOF
>> trajin in.crd
>>
>> closestwater 50 :15_at_SG oxygen
>> image :WAT byres
>> rms first mass :13-146_at_CA,C,N:176-309_at_CA,C,N
>> trajout in_trajout.crd
>>
>> go
>> EOF
>>
>> Can any one spot a problem, suggest a fix, or suggest an alternate method
>> to preserve the waters that enter the active site while stripping the
>> others? Thanks.
>>
>
> I think you should do "image" command before the "closestwater" command.
> Best,
>
> Jianyin
>

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