On 6/11/2007 4:27 AM, David van der Spoel wrote:
Sheyore Omovie wrote:
Thanks Yang,
Each of the residues in my *.gro have more H-atoms than in *.top. I
added the 21 H-atoms in [molecules] section of *.top. But grompp
still came up with the ff error: No such molecule type.
Do i have to edit [m
What actually is it that you want to know about?
Your email doesn't really specify anything that you are trying to find out.
Are you wanting to maybe be able to neutralise the change in a system using
genion? Have you looked at the tutorials and checked "genion -h"?
-Original Message
Sheyore Omovie wrote:
Thanks Yang,
Each of the residues in my *.gro have more H-atoms than in *.top. I
added the 21 H-atoms in [molecules] section of *.top. But grompp still
came up with the ff error: No such molecule type.
Do i have to edit [moleculetype] section too?
Rgds
John
Please do
Thanks Yang,
Each of the residues in my *.gro have more H-atoms than in *.top. I added
the 21 H-atoms in [molecules] section of *.top. But grompp still came up
with the ff error: No such molecule type.
Do i have to edit [moleculetype] section too?
Rgds
John
From: Yang Ye <[EMAIL PROTECTED]>
Alan Dodd wrote:
Hello all,
A recent simulation has been running on a cluster for a couple of weeks.
5.something-ns in it crashed due to a hardware glitch. All perfectly
understandable so far.
The strange thing is, using tpbconv now results in a .tpr that crashes in the
first step due to mas
On 6/10/2007 8:54 PM, Sheyore Omovie wrote:
You're right, the total charge is zero. While creating *.top, pdb2gmx
did not recognise some hydrogen atoms in my pdb file (HA atom type in
particular).
I had to use -ignh to ignore the H-atoms.
No. This is not the reason why there are different num
Hi, Saf
We use a special bond for heme, specified in specbond.dat. Check the
mailing list archive.
Regards,
Yang Ye
On 6/10/2007 9:17 PM, Shahrokh Safarian wrote:
Dear Yang YE
Thank you very much for your kind cooperation. I did upload my pdb file
to prodrg but there were two problems:
1) t
You're right, the total charge is zero. While creating *.top, pdb2gmx did
not recognise some hydrogen atoms in my pdb file (HA atom type in
particular).
I had to use -ignh to ignore the H-atoms.
Can I just add this atoms to the *.top like u've stated below, or do I need
to edit *.rtp to include
This is called parameterization.
http://wiki.gromacs.org/index.php/Parameterization
For small molecule, you can opt for PRODRG for GROMOS/GROMACS force
fields; or Antechamber for AMBER force field.
Once you obtained the topology, convert them back to the format in the
rtp file according to the
Dear colleagues
As you know if we want to introduce a new molecule into Gromacs, the
related parameters for that molecule (e.g. [atoms], [bonds], [pairs],
[dihedrals] and so on) should be inserted to the Gromacs rtp file. In
the Gromacs user's manual (page 100) an example for these types of
topolo
There is 2312-2291=21 more atoms in your structure file than in the
topology file. If it is due to genion, it shall be less. There might be
other mistakes in previous steps.
Anyway, to make them match, just count how many molecules you have in
the system. The last section in your top file shal
mahbubeh zarrabi wrote:
dear all
I want to insert protein in bilayer. how can i put
position of protein in x,y, and z ralative to the
bilayer by editconf?
best regards
editconf -h
No need to miss a messa
dear all
I want to insert protein in bilayer. how can i put
position of protein in x,y, and z ralative to the
bilayer by editconf?
best regards
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