On 9/10/17 2:38 PM, Roshan Shrestha wrote:
For my system which has a net charge of -3, I wanted to add NaCl to a
concentration of 0.1 M. So, I used *gmx genion -s ions.tpr -o 1aml_ions.gro
-p topol.top -pname NA -nname CL -np 3 -conc 0.1 -neutral*
I've got a feeling that to make my system
For my system which has a net charge of -3, I wanted to add NaCl to a
concentration of 0.1 M. So, I used *gmx genion -s ions.tpr -o 1aml_ions.gro
-p topol.top -pname NA -nname CL -np 3 -conc 0.1 -neutral*
I've got a feeling that to make my system neutral, I should be using only *gmx
genion -s
Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to
neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro
-pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand
Dear Gromacs users,
I am working with membrane proteins. I have build my membrane-protein
systems with a layer of water bed on top and bottom of the membrane. Now,
I would like to add a specific concentration of KCl to bottom layer of the
water bed. Can anybody suggest me a way to add ions to a
Hi,
Dunno, never tried the walls code.
Mark
On Thu, Jul 2, 2015 at 11:37 PM João Martins joaomartins...@gmail.com
wrote:
As a completely pointless point since Mark just explained why it doesn't
make much sense to do it, you can achieve the same by separating your
waters in the [ molecules ]
Hi,
Your membrane is probably in the x-y plane, so you just insert ions
everywhere and delete from the .gro file all that have a z coordinate
bigger than whatever value aligns with the bottom of your membrane, and
correct the number of atoms in the .gro and .top file accordingly.
This won't help
Justin,
I have used the paramchem software as suggested by you. I
submitted my pdb file and CGENFF gave a .str file as output. Now could you
please tell me how to proceed to obtain the .itp file? Also is it sensible
to use SWISSPARAM since it gives .itp from .mol2 directly? Once I have
On 11/19/14 4:33 AM, soumadwip ghosh wrote:
Justin,
I have used the paramchem software as suggested by you. I
submitted my pdb file and CGENFF gave a .str file as output. Now could you
please tell me how to proceed to obtain the .itp file? Also is it sensible
Use our converter;
On 11/18/14 1:47 AM, soumadwip ghosh wrote:
Dear Justin,
thanks for your reply. I really dont know how to create
the .itp file from the .pdb file of the TMA cation. Do I need a topology
builder? After making the .itp file, how should I proceed? If I have to add
it by
Dear all,
I am currently working on double stranded DNA aggregation
and I require to add tetramethyl ammonium ions in my system. I know there
are certain files to be modified in the force field directory for this
purpose but I dont know which files. I am using Gromacs 4.6.5 and
Dear Justin,
thanks for your reply. I really dont know how to create
the .itp file from the .pdb file of the TMA cation. Do I need a topology
builder? After making the .itp file, how should I proceed? If I have to add
it by genion, then I guess the tma.itp must be a part of the
Hi,
Use genion -neutral and let gromacs do that hard work.
Regards,
On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com
wrote:
Dear users,
My protein is a trimer and I want to run md : on binding of a peptide
(chain-D) to this trimer (chain-ABC).
Therefore, I have
When you bundle up the system run file (.tpr), using gmx grompp, to pass to gmx
genion, it will list in the terminal output the net charge of the entire system.
Additionally, you could simply use the -neutral option and not specify the
number of ions required, the script will work that out for
hi GMX users
The output of pdb2gmx told me that the protein-ligand complex has a net charge
of 0(zero)
but at the last line of my[ atoms ] directive in topol.top;qtot 2.749e-06 .
be read .
1)What does this mean?
2) if my system has a net charge of 0(zero),must iadd ions to my system for
On Jan 26, 2014 10:57 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com
wrote:
hi GMX users
The output of pdb2gmx told me that the protein-ligand complex has a net
charge of 0(zero)
but at the last line of my[ atoms ] directive in topol.top;qtot
2.749e-06 . be read .
1)What does this mean?
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