Thank you very much Dan for your detailed reply. I will try to do what
you described. To date I have always performed the extraction of
trajectory with the 10 closest waters included using the "closestwaters"
command in ptraj. The point is that the calculation of distances is
rather slow, that is why I wanted to run it in parallel using cpptraj.
Unfortunately I find that the "closestwater" command is not included in
cpptraj. The possibility of separately indicating the "strip" mask and
"distance calculation" mask would include this valuable possibily. In my
case I am trying to to include certain water molecules in MMPBSA
calculations.
Thank you very much again for the support,
all the best
Alfredo
Para: AMBER Mailing List <amber.ambermd.org>
>
> Hi,
>
> On Mon, Apr 16, 2012 at 3:57 PM, Alfredo Quevedo
> <alfredoq.fcq.unc.edu.ar> wrote:
>> (LIG) with the corresponding 10 WAT molecules. How I am supossed to
>> indicate cpptraj to conserve the rest of the receptor and calculate WAT
>> distances just based in LIG residue?
>
> Currently it is not possible in ptraj or cpptraj to specify separate
> masks for stripping and distance calculation in the closest command,
> although this would be a nice feature and may be included in an
> upcoming release, maybe a patch.
>
> Currently the only way I can think of to do this is a bit involved but
> could probably be made somewhat tractable through scripting. You could
> generate PDB files of the ligand with the 10 closest molecules,
> generate corresponding PDB files of the receptor, then concatenate
> them outside of cpptraj and convert them back into a trajectory. So
> for example to generate the ligand/water and receptor PDBs in one
> step:
>
> trajin Solvated-trajectory.mdcrd
> closest 10 :LIG first closestout archive.dat
> outtraj Ligand-10closest.pdb pdb multi
> unstrip
> strip :WAT,LIG outprefix strip
> outtraj Receptor.pdb pdb multi
>
> This will generate two pdb files per frame, one named
> Ligand-10closest.pdb.X and the other named Receptor.pdb.X, where X is
> the frame number. Note the unstrip command, which undoes the effect of
> the closest command so that the receptor is present for 'strip'. You
> can concatenate each of these PDBs together for each frame (removing
> the END cards) to generate frames with receptor/ligand/10 waters using
> a script like (assuming 10 frames):
>
> bash:
> for (( frame=1; frame <= 10; frame++)) ; do
> cat Receptor.pdb.$frame Ligand-10closest.pdb.$frame | grep -v "END
> " > Output.pdb.$frame
> done
>
> Then you can generate a parm containing the receptor, ligand, and 10
> waters either with tleap or you can do it with cpptraj. For the
> following example I have a system which the receptor is residues 1 -
> 268, the ligand is residue 269, and the first 10 water molecules are
> 270-279:
>
> parm Solvated.parm7
> parmstrip !(:1-279)
> parmwrite out closest.Solvated.parm7
>
> Substitute your actual parm name here. For this example a parm
> 'closest.Solvated.parm7' would be generated containing residues 1 to
> 279. Adjust the mask accordingly for your system.
>
> Last, you would combine all of the Receptor/ligand/10 water PDBs back
> into a trajectory.
>
> bash:
> echo "parm closest.Solvated.parm7" > cpptraj.in
> for (( frame=1; frame <= 10; frame++)) ; do
> echo "trajin Output.pdb.$frame" >> cpptraj.in
> done
> echo "trajout combined.nc netcdf nobox" >> cpptraj.in
>
> cpptraj -i cpptraj.in
>
> At this point you should have a topology (closest.Solvated.parm7) and
> netcdf trajectory (combined.nc) containing the receptor, ligand, and
> 10 closest waters. Phew!
>
> Thanks for the good feature suggestion. Let me know if you have any
> more troubles or if I can be of any more help.
>
> -Dan
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ----- Terminar mensaje reenviado -----
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
--
************************************************************************
Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 17 2012 - 06:00:06 PDT
