Dear Jason,
Following your instructions I successfully managed to strip extra solvent molecules.
However, I am having a doubt and hope you can clarify it . As far as I know in PBC the molecules lost from one side are gained from other end. Hence, the water molecules lost from one end due to movement while simulating will appear from other end. This should result in shuffling of water molecules surrounding the protein. Now, as I have stripped water molecules i.e. from 7150-13526 is there a possibility that some of them were taking part in interaction in one or more trajectories?
Regards,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Wednesday, April 02, 2014 7:54 PM
To: amber.ambermd.org
Subject: Re: [AMBER] truncatiing water molecules
On Wed, 2014-04-02 at 19:36 +0800, Nitin Sharma wrote:
> Dear amber users,
>
> I have two trajectories with same number of protein residues with
> similar connectivity along with one ligand. However, the they have
> different number of water molecules. The reason for this is that I
> have created these files by stripping terminal protein residues.
>
> I tried to strip water molecules using following script:
>
> trajin 2NL9_046_strip.mdcrd
> reference 2NL9_046_strip_test1.pdb [refpdb] rms .CA,C,N ref [refpdb]
> strip "!(:1-150<:12.0)&:WAT" outprefix stripped_2NL9_b_046_b trajout
> /hpctmp/a0068362/MCL1_combined_test/2NL9_046_strip_b.mdcrd
> netcdf nobox
>
> however, I am getting different number of water molecules in two
> protein and also less than 50 water molecules in both cases.
>
> Is there any way I strip certain number of water molecules from each
> file so that the files for different protein are same? While solvating
> I used command "solvateoct comp TIP3PBOX 12.0"
Take the system that has more waters. Find out how many more waters that system has (you can typically just look at the number of residues, which is NRES if you use the "printPointers" command in ParmEd). Let's suppose one system has 10 more waters than the other system: strip the last 10 residues from the system with 10 more waters using the command you've printed above.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 06:30:02 PDT
