[gmx-users] PRODRG topology server problem!

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Mon Sep 23 18:47:43 CEST 2002

Hi Chen

I'm performing some simulations with calix[4]arenes and I'm using GROMACS
too. About the hydrogens, the other guys said everything. About the
solvents, you can user another ones, but you need to construct your own
topology files. I'm using acetonitrile and to make the topology for it I put
the PDB file of it in PRODRG. The result was good, but the charges assigned
was not. Then I searched for pappers with the parameters for acetonitrile
and I found it(sigma, epsilon and charges). I think this way is the best

Alexandre Suman de Araujo
IFSC - USP - São Carlos
UIN: 6194055
----- Original Message -----
From: <pqchen at eyou.com>
To: <gmx-users at gromacs.org>
Sent: Sunday, September 22, 2002 10:53 PM
Subject: [gmx-users] PRODRG topology server problem!

> Dear all:
>   I am a student of Nankai University in China!
>   Recently I want to use gromacs program to study calix[4]pyrrole
> 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
> the gromacs .top file,there is none of the hydrogens.And my molecule +
> 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
>                                                              Chen PeiQuan
> --http://www.eyou.com
> --Îȶ¨¿É¿¿µÄÃâ·Ñµç×ÓÐÅÏä  ÓïÒôÓʼþ  Òƶ¯ÊéÇ©  ÈÕÀú·þÎñ
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