Hi,
Thanks for comments.
PTRAJ is able to generate pdb from chamber prmtop and inpcrd, BUT with a
message on appeared on screen:
"WARNING in scanDouble: ...scanning chrg"
and in the ptraj.out:
PRMTOP does not contain %FLAG TITLE
There were errors upon reading parm file!!!
As for vmd, the lasted 1.9beta version and earlier version cannot understand
chamber prmtop, but it can, however understand the file if CTITLE is
replaced with TITLE. But, with edited chamber prmtop and later on loaded in
the inpcrd, the atoms of the system lost their connectivity.
Thanks and regards,
colvin
On Wed, Mar 2, 2011 at 12:30 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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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> > >
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>
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Received on Tue Mar 01 2011 - 23:30:03 PST
