AMBER Archive (2009)

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

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Fri May 15 2009 - 10:54:17 CDT

Hi,

The second is from xleap and the first is from vmd(saving as pdb)

I am applying different changes within vmd so it would be much easier to be
able to save directly from VMD

Best

Jorgen

On Fri, May 15, 2009 at 4:17 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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
>
>
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