[gmx-users] PRODRG topology server problem!
lindahl at stanford.edu
Mon Sep 23 04:05:58 CEST 2002
pqchen at eyou.com wrote:
> I am a student of Nankai University in China!
> Recently I want to use gromacs program to study calixpyrrole molecule!But
>when I use the PRODRG topology server to generate the .top file,there is a
>error ocur!The program file can't add the exatly hydrogens to my molecule!In
>the gromacs .top file,there is none of the hydrogens.And my molecule + added
>show that the hydrogens on the Nitron is absent.Can somebody can help me!
> BTW:Can gromacs program use other solvents except the water solvent?
> sincerely yours
> Chen PeiQuan
I don't use PRODRG myself, but Daan is reading this list, so I'm sure
he'll reply too.
In principle, you can use any solvent you want with Gromacs; the genbox
places just needs a file with coordinates of equilibrated solvent
molecules. The distribution
already includes coordinates for decane, DMSO, methanol, SPC water (you
can use these
for any 3-particle water model, though), TIP4P water and a mixture of
water and urea.
We'd be happy to include more coordinates if you create any other
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