Hi Colvin,
You won't be able to modify the chamber prmtop by hand since there are a
number of differences, all of which are technically legal given the prmtop
format I might add but a number of programs, most due to the complexities of
reading Fortran format strings in other languages, do not properly implement
the prmtop format.
ambpdb was unfortunately never updated for Chamber prmtops. However ptraj
(from AMBER 11) should, I believe, work. You can use this to make a pdb
file. E.g.
$AMBERHOME/bin/ptraj foo.prmtop
trajin foo.inpcrd
trajout foo.pdb
go
As for VMD, Mark Williamson may need to chime in here. I though the very
latest version of VMD had been updated for Chamber prmtops but I might be
wrong. You can try editing the CTITLE to TITLE and see if VMD will process
it then, but I would be surprised. If that does not work then the
alternative is just to use the original psf file from which you built the
prmtop. VMD will let you load a charmm psf (or pdb if you want) and then
into this you can load an AMBER mdcrd file etc. As long as the atoms counts
match and are in the same order, which they should be, it should work fine.
Good luck,
Ross
> -----Original Message-----
> From: colvin [mailto:colvin4367.gmail.com]
> Sent: Tuesday, March 01, 2011 7:58 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] CHAMBER prmtop
>
> Hi,
>
> i tried to replace
>
> %FLAG CTITLE
>
> to
>
> %FLAG TITLE
>
> but it gave this:
>
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/11/03 Time = 12:02:08
> At line 249 of file _ambpdb.f90 (unit = 10, file = '1.prmtop')
> Fortran runtime error: Expected REAL for item 2 in formatted transfer, got
> INTEGER
> (5e16.8)
>
> ^
>
> i then added %FLAG TITLE before %FLAG CTITLE, it gave the same error
> message as well.
>
>
> pls assists.
>
>
> Thanks and regards,
> colvin
>
> On Wed, Mar 2, 2011 at 11:51 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > ERROR: Flag "TITLE" not found in PARM file
> > > any workaround for this?
> >
> > Maybe add a title in the prmtop using a text editor and deductive
> > skills. Other missing flags might be more problematic to simulate,
> > but title should be easy.
> >
> > Bill
> >
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Received on Tue Mar 01 2011 - 21:00:03 PST
