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---- trajin out1.mdcrd strip :211-9199 center :1-210 image center trajout strip.mdcrd ---- ptraj2.in --- trajin out1.mdcrd 1 1 1 trajout top PDB center :1-210 strip :211-9199 --- The closest command in ptraj has the logical effect that it modifies the state of the system, ie., new numbering of atoms. Although in my output 'out.mdcrd' the 10 closest waters appeared immediately next to the solute, the remaining waters (211-9199) follows it. I do not want this remaining waters to be included for mmpbsa calculations. The attempt I did above is a strategy of first implementing the closest command, then the next ptraj script to strip the unwanted waters (far distant from ligand). Another strategy I did was to issue both closest and strip in one single script as follows: B)Strategy-2 close2.in ------- trajin in.mdcrd trajout out1.mdcrd closest 10 :200 image :WAT byres rms first mass :1-199 strip :211-9199 ----- Here is the error: Mask [:211-9199] represents 0 atoms !!!NO ATOMS DETECTED!!! Understanding how closest command works, it does change the state of the system, particularly the numbering, as evidenced of its inability to detect the mask 211-9199. If that is the case, how to strip the unwanted waters? My assumption is that since the closest command designates new atom numbering, using the strip command will not detect any specified water atoms that I desired to remove from the trajectory. This could also be the reason why am I viewing unwanted long lines in vmd. Alternatively, I read from the forum about this simple script: C)Strategy-3 ---- trajin out1.mdcrd strip "(:200 >.5.0)" trajout strip.mdcrd ----- The script strip all atoms further than 5 Angstroms from the ligand (:200). Problem with this is that my input has the protein + ligand, so what the script does is it strip all atoms (including protein and water) located further than 5 angstroms. On the lighter side, apart from those 3 strategies I was able to view in vmd the 'out1.mdcrd' (protein+ligand + ten closest H2O + remaining bulk tip3p H2O) using a new topology created by ambpdb using one snapshot taken from out1.mdcrd. There is no problem viewing this trajectory containing all waters in box, the problem goes to strip water trajectory. I digress .... it is a fact that handling water molecules is challenging. I believe there is a solution to these issues. Amor --- On Fri, 20/8/10, Amor San Juan <amorsanjuan.yahoo.com> wrote: From: Amor San Juan <amorsanjuan.yahoo.com> Subject: PTRAJ: closest & strip in one script or separate To: "AMBER Mailing List" <amber.ambermd.org> Date: Friday, 20 August, 2010, 5:33 PM Is it possible to create a script in ptraj wherein both closest and strip commands are present? The script I used for closest: closest 10 :200 image :WAT byres rms first mass :1-199 The output trajectory (in order as it appears) contains : protein ligand waters(10) closest remaining tip3p water The script was able to find the ten closest waters near the ligand (:200) and write it in the output immediately afer the protein+ligand. The problem is the unselected waters (thousands and thousands) are still in the output. I tried to experiment on adding the strip command in above script but was not successful. Also, the other way around is from the output above I make a separate ptraj script to strip the waters 211-9199. Both are not successful. My aim is to get an output trajectory (P+L+W10), such that P=protein,L=ligand,W10=ten closest waters. And feed this into MMPBSA for binding energy calculation. Amor _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Aug 23 2010 - 04:30:03 PDT