AMBER Archive (2009)

Subject: Re: [AMBER] xleap reading hydrogens giving error

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri May 15 2009 - 09:17:04 CDT

On Fri, May 15, 2009, Jorgen Simonsen wrote:
>
> I am using vmd visualize my md simulation if I save a pdb file from vmd and
> want to build parameter file or just load it into xleap it cannot read the
> hydrogens as VMD is saving it differently from what xleap wants to read :
>
> ATOM 8 2HB GLN 1 41.513 -7.459 22.401 1.00
> ATOM 9 3HB GLN 1 40.425 -6.562 21.370 1.00
>
> ATOM 8 2HB GLN 1 41.535 -7.381 22.326 1.00 0.00
> ATOM 9 3HB GLN 1 40.259 -6.537 21.418 1.00 0.00

I'm confused: where did the two pdb snippets above come from? The second
looks correct, the first incorrect.

Also, why do you need to do this? Are you changing the structure inside VMD?
Why not just use ptraj to create the pdb files?

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber