On 16/04/2011 6:05 PM, ahmet yıldırım wrote:
Dear Justin,
I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for
each EDO moleculeusing prodrg web server. Then I created 6 .itp files
as EDO1.itp, EDO2.itp.EDO6.itp.
Why? The fragment
[molecules]
EDO 6
is what specifies s
Dear Justin,
I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for eachEDO
molecule using prodrg web server. Then I created 6 .itp files as EDO1.itp,
EDO2.itp.EDO6.itp. I changed residue numbers. But I have Fatal Error
"moleculetype EDO is redefined". Am I on the wrong track?:
ahmet yıldırım wrote:
Dear Justin,
Thanks for your valuable helps. How should I rearranged the conf.gro
file for 6 EDO ligand? is the following conf.gro mistake?
Well, it's certainly not working, is it? You only have one EDO molecule shown
here. Is this the only one? If it is, then y
Dear Justin,
Thanks for your valuable helps. How should I rearranged the conf.gro file
for 6 EDO ligand? is the following conf.gro mistake?
*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
5354
2GLN N1 1.458 -1.158 0.739
2GLN H12 1.520 -1.083 0.763
...
485HO
ahmet yıldırım wrote:
Dear Justin,
I built .rtp entries for two ligands using
(http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top
the following parts:
#include "TRS.itp"
#include "EDO.itp"
Well, either pdb2gmx built the molecules into your topology or you're #including
Dear Justin,
I built .rtp entries for two ligands using (
http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the
following parts:
#include "TRS.itp"
#include "EDO.itp"
TRS 1
EDO 6
Furthermore I added the number of atoms (20) in the second line of t
ahmet yıldırım wrote:
Dear users,
pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordin
Dear users,
pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordinate file (solvated.gro, 10
Hi Chitrita,
Please copy-paste the exact error and the command line in both cases
(working and not working). Also, what platform are you working on? Did
you by chance edit the .mdp file under windows?
Cheers,
Tsjerk
On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy
<[EMAIL PROTECTED]> wrote:
I want to perform MD Equilibration run under position restrained for
200ps. Bond
distances were constrained using the LINCS (Linear Constraints) algorithm,
the water molecules were restrained using the SETTLE algorithm. In order to
do this I have modified nsteps in original pr.mdp file. Following i
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