Indeed this seems likely. I was able to add 125 urea and solvate w/out
incident doing it in two steps.
Thanks again,
Ken
On Apr 23, 2009, at 1:31 PM, Justin A. Lemkul wrote:
Ken Rotondi wrote:
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
I don
Ken Rotondi wrote:
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
I don't know that it's a bug per se, more of a limitation. The program is
trying to solvate the structure, as well as cram in X molecules of something
else all at once and probably
Dear Justin, All,
Yes, running as two separate steps works, is this a known genbox bug?
Ken
-works-
pdb2gmx -f diala.pdb -o diala.gro -p diala.top -ff G53a6 -ignh
editconf -f diala.gro -o dialabox.gro -bt dodecahedron -box 3.1
genbox -cp dialabox.gro -ci urea.gro -nmol 1 -o dialaurea.gro -p
Ken Rotondi wrote:
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
Does it work if you use -ci to insert your molecule, then in a separate step,
use -cs to solvate?
-Justin
On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
Which version of Gromacs? There was a bug in
Sorry, vers 4.0.4 here on an intel macbook running OSX.5.5
On Apr 23, 2009, at 11:06 AM, Justin A. Lemkul wrote:
Which version of Gromacs? There was a bug in genbox that was fixed
for version 4.0.4.
-Justin
Ken Rotondi wrote:
Hello All,
I have managed to get urea into the G53a6 ffield w
Which version of Gromacs? There was a bug in genbox that was fixed for version
4.0.4.
-Justin
Ken Rotondi wrote:
Hello All,
I have managed to get urea into the G53a6 ffield with suitable
adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying
to use the resulting urea.gro
Hello All,
I have managed to get urea into the G53a6 ffield with suitable
adjustments to the appropriate .pdb, .rtp, and .hdb files. I am trying
to use the resulting urea.gro file (I have also tried with a urea.pdb
file generated from the urea.gro file using pdb2gmx) in genbox using
the -
Hi Mark,
From the log it seems you're trying to solvate your protein (-cp
gmx.pdb) with your protein (-cs gmx.gro)! Read the manual on genbox...
Tsjerk
On 7/16/07, Mark Zottola <[EMAIL PROTECTED]> wrote:
I am trying to run genbox and am getting a segmentation fault. After
running pdg2gmx, I
I am trying to run genbox and am getting a segmentation fault. After
running pdg2gmx, I generated a gro file from the pdb outfput from pdb2gmx
using editconf. I then ran the editconf which seemed to run without
problem. Then I tried to use genbox. It was at this point I received a
segmentation
Li, Yun wrote:
Thanks for getting back to me so quickly. I am following this tutorial:
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm
It seems to be very straight forward. However, I can't overcome my
problem. Here is the output from genbox:
:-) G R O M A C
Thanks for getting back to me so quickly. I am following this tutorial:
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm
It seems to be very straight forward. However, I can't overcome my
problem. Here is the output from genbox:
:-) G R O M A C S (-:
Li, Yun wrote:
Hi,
I was very excited to discover Gromacs and decided to learn by following
a few tutorials I found online. However, I ran into a problem: After
filling up the simulation box with SPC water using genbox, the program
backed up the topology file into another file with its nam
Hi,
I was very excited to discover Gromacs and decided to learn by following
a few tutorials I found online. However, I ran into a problem: After
filling up the simulation box with SPC water using genbox, the program
backed up the topology file into another file with its name flanked by
#, and
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