[gmx-users] PRODRG topology server problem!

[Erik Lindahl]

pqchen at eyou.com wrote:

>Dear all:
>  I am a student of Nankai University in China!
>  Recently I want to use gromacs program to study calix[4]pyrrole 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
>hydrogens
>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
>
Hi Chen,

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 
program that
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 
solvent :-)

Cheers,

Erik