[gmx-developers] Re: pdb2gmx, -water option, and non-standard models

[Joshua L. Phillips]

Thanks Daniel. I've been using the solution suggested by Berk (echo 3 |
pdb2gmx ...) to do this for quite awhile, but editing the topology file
using sed is probably a little safer since some forcefields have more
(fewer) water models to consider than others.

What I imagine being the best solution is something like:
pdb2gmx -ff amber99sb -water tip4pew ...

I think it is reasonable to expect that a user can edit the topology
file themselves if they choose to use a water model that is not packaged
with Gromacs. However, I imagine most users would expect all water
models packaged with Gromacs to be listed in the enumeration.

Maybe the problem is just that tip4pew is missing from the enumeration? 

-- Josh

On Fri, 2011-04-15 at 12:00 +0200, gmx-developers-request at gromacs.org
wrote:
> Date: Fri, 15 Apr 2011 11:58:29 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] pdb2gmx, -water option, and non-standard
>         models
> To: Discussion list for GROMACS development
>         <gmx-developers at gromacs.org>
> Message-ID: <4DA816C5.7010209 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> On 2011-04-15 11.49, Berk Hess wrote:
> > On 04/15/2011 11:40 AM, David van der Spoel wrote:
> >> On 2011-04-15 11.37, Daniel Larsson wrote:
> >>> An easy solution to "choose" the water model is to just edit the
> >>> output from pdb2gmx.
> >>>
> >>> sed -i
> >>>
> 's#amber99sb-ildn.ff/tip3p.itp#/path/to/custom/topology/tip4pew.itp#'
> >>> topol.top
> >>>
> >>> Daniel
> >>>
> >>>
> >>> On Apr 14, 2011, at 19:43 , Joshua L. Phillips wrote:
> >>>
> >>>> Hi All,
> >>>>
> >>>> pdb2gmx is a great tool and I really like the flexibility to
> specify
> >>>> different forcefields using the -ff option (great for scripting)!
> >>>>
> >>>> However, when selecting water models, I was recently disappointed
> that
> >>>> the water selection option (-water) was an enumeration because it
> lacks
> >>>> the flexibility to test novel water models. For instance, even a
> highly
> >>>> regarded model like "tip4pew" isn't specified in the enumeration.
> >>>>
> >>>> Maybe the -water option could be changed to a string (similar to
> >>>> -ff) in
> >>>> order to allow easy selection of "non-standard" water models? I
> am not
> >>>> familiar with the technical issues that might need to be
> addressed, so
> >>>> this is just a humble suggestion.
> >>
> >> There is a file in your favorite force field directory containing
> the
> >> water models. Just add it there.
> > No, this is about the pdb2gmx -ff option not supporting it.
> >
> > I don't know if:
> > echo tip4pew | pdb2gmx
> > would do it.
> >
> > Berk
> 
> No.
> 
> if you do
> echo 3 | pdb2gmx -f protein -ff amber99sb
> it works.
> This is indeed a bug in pdb2gmx.
> 
> >>>>
> >>>> Thanks!
> >>>>
> >>>> --
> >>>> Joshua L. Phillips
> >>>> Ph.D. Candidate
> >>>> School of Engineering
> >>>> University of California, Merced
> >>>>
> >>>> Email: jphillips7 at ucmerced.edu
> >>>> Phone: (209) 723-0921
> >>>>
> >>>> --
> >>>> gmx-developers mailing list
> >>>> gmx-developers at gromacs.org
> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> >>>> Please don't post (un)subscribe requests to the list. Use the
> >>>> www interface or send it to gmx-developers-request at gromacs.org.
> >>>
> >>
> >>
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se