Maybe you can get a pdb without using ptraj with ambpdb
or ambmask [...] from a restart file and then check your ligand
to ensure yourself what's happening there. To remove waters,
you can edit with vi your pdb out or just grep
the desired atoms (like the ligand). You can also attempt to read
directly a topology file and a set of coordinates with any viewer
able to treat with these files ( pymol or, vmd?).
2007/4/23, alfredoq.fcq.unc.edu.ar <alfredoq.fcq.unc.edu.ar>:
>
> Dear Amber users:
> I am having troubles to prepare the snapshots for mm_pbsa
> analysis. I have the trajectory file and the corresponding prmtop file,
> wich I
> can visualize in VMD without problems. The point is that after striping
> the
> waters and ions with ptraj, and obtaining the new desolvated and deionized
> prmtop files, when I try to check the new trajectory, I find that the
> ligand
> atoms are all missplaced, with corrupted binding distances, angles and
> lenghts.
> Obviously, the snapshots for mm_pbsa are also corrupted. I have checked
> several
> times the integrity of the ligand prepin and frcmod file, but everything
> seems
> to be ok. Does anyones have experienced this kind of problems before,
> Thank you in advance for the help
>
> Best Wishes
>
> Alfredo Quevedo
>
>
> ----------------------------------------------------------------
> Facultad de Ciencias QuĂmicas - Universidad Nacional de CĂrdoba
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 25 2007 - 06:07:21 PDT
