I think what's not clear is that a trajectory contains many snapshots, and
you say you want to make a pdb from it. Cpptraj did that, for each frame.
If you want a specific frame to start your gb md, use that one as input to
leap for the GB setup.
On May 3, 2017 3:26 AM, "Ramin Salimi" <ramin.salimi01.utrgv.edu> wrote:
> Dear All
>
> If I have a solvated trajectory at the end of my simulation, and now would
> want to run implicit solvation GB/SA model based on that trajectory
> previously obtained from explicit solvent, how do I get that done?
>
>
> In fact, I wrote the following script in cpptraj and the pdb file it gave
> me had 8000 models corresponding to the 8000 frames of my solvated
> trajectory.
>
> I am confused here. My plan was to create a pdb from that solvated
> trajectory. Then using tleap, and switching to mbondi3, get my starting
> parameter and coordinate files to run GB/SA method with igb=8.
>
>
> Can you please give me some insight on what I did/am doing wrong? Is there
> any other way I should be pursuing to implement implicit solvation method
> based on a solvated trajectory?
>
>
> parm revnelson.smd.prmtop
>
> trajin smd.mdcrd
>
> strip :WAT
>
> center :1-24 mass origin
>
> image origin center familiar
>
> trajout smdgb.pdb pdb nobox
>
>
> My deep apologies if this looks simple
>
> Regards
>
> Ramin
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 03 2017 - 03:30:02 PDT
