[gmx-users] Minimization of a drug alone

[Daan van Aalten]

Dear Tanos

The PRODRG server by default run a GROMACS EM on your compound

these are the GMX grompp input file that the server uses:


 cpp                 =  /lib/cpp
 define              =  -DFLEX_SPC
 constraints         =  none
 integrator          =  steep
 nsteps              =  50000
 ;
 ;       Energy minimizing stuff
 ;
 emtol               =  1
 emstep              =  0.01

 nstcomm             =  1
 ns_type             =  grid
 rlist               =  1
 rcoulomb            =  1.0
 rvdw                =  1.0
 Tcoupl              =  no
 Pcoupl              =  no
 gen_vel             =  no
 pbc                 =  no



cheers

Daan



On Thu, 5 Jun 2003, [iso-8859-1] Tanos C. C. França wrote:

>             Hi folks,
>             Is it possible to perform a em of a drug alone (do not
> docked into a protein ???) in gromacs ?? I have been trying but  grompp
> do not recognize the .top file I generated in the PRODRG server. Is
> there any other way of generating the .top file of my DRG ??????
>             Thanks a lot in advance.
>             Tanos C. C. Franca.
>
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.483 / Virus Database: 279 - Release Date: 19/05/2003
>
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O