Re: [gmx-users] Adding ions

2017-09-10 Thread Justin Lemkul
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

[gmx-users] Adding ions

2017-09-10 Thread Roshan Shrestha
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

[gmx-users] Adding ions

2016-05-22 Thread mohammad r
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

[gmx-users] Adding ions to membrane protein system

2015-07-02 Thread anu chandra
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

Re: [gmx-users] Adding ions to membrane protein system

2015-07-02 Thread Mark Abraham
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 ]

Re: [gmx-users] Adding ions to membrane protein system

2015-07-02 Thread Mark Abraham
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

Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-19 Thread soumadwip ghosh
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

Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-19 Thread Justin Lemkul
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;

Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-18 Thread Justin Lemkul
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

[gmx-users] adding ions in Gromacs 4.6.5

2014-11-17 Thread soumadwip ghosh
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

Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-17 Thread soumadwip ghosh
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

Re: [gmx-users] adding ions in the genion for multimeric proteins

2014-09-03 Thread rajat desikan
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

Re: [gmx-users] adding ions in the genion for multimeric proteins

2014-09-03 Thread Dallas Warren
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

[gmx-users] Adding Ions step

2014-01-26 Thread Mahboobeh Eslami
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

Re: [gmx-users] Adding Ions step

2014-01-26 Thread Mark Abraham
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?