On Thu, Mar 10, 2016 at 1:55 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> It does not seem, from the options in the manual, that cpptraj has a way
> to produce an associated parameter file in the GROMACS format. This
> confuses me, because I am unsure what good a GROMACS trajectory would be
> without the associated topology file.
Cpptraj is in the trajectory analysis business. For convenience it can
output Amber topology files because I am very familiar with the
format; I've tested this functionality very thoroughly so I have
confidence that it works well. I am much less familiar with other
topology formats as I work with them far less often. This is why in
cpptraj they are mostly read-only (and Charmm PSF is noted as 'Limited
PSF Write', Amber 15 manual, Table 29.2). I leave most
topology-related manipulation to parmed since that is it's job.
> Under parmwrite, the manual seems
> to imply that one can select an alternative format for the parameter
> file (but the manual gives no examples of what formats are possible). Is
Again, see table 29.2 in the Amber 15 manual.
> it possible to convert Amber topology files to GROMACS style using the
> parmwrite keyword in cpptraj?
As Hai recommended, use parmed. Hope this helps,
-Dan
>
>
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Thu Mar 10 2016 - 14:00:03 PST
