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

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 15 11:40:19 CEST 2011

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.
>> Thanks!
>> --
>> Joshua L. Phillips
>> Ph.D. Candidate
>> School of Engineering
>> University of California, Merced
>> Email: jphillips7 at ucmerced.edu
>> Phone: (209) 723-0921
>> --
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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

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