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"
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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Received on Wed Apr 02 2014 - 05:00:07 PDT
