Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread Justin A. Lemkul
SHIVANGI NANGIA wrote: Hi, Thanks so much for the prompt help. Yes, I did realize that methanol as solvent was not updated in the .top file. I had to fix the .top file manually. When I add ions using genion I replace methanol. As a test I tried setting up the whole system with the change

Re: Re: Re: Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread SHIVANGI NANGIA
Hi, Thanks so much for the prompt help. Yes, I did realize that methanol as solvent was not updated in the .top file. I had to fix the .top file manually. When I add ions using genion I replace methanol. As a test I tried setting up the whole system with the change that instead of 8 hydroxide i

Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread Justin A. Lemkul
SHIVANGI NANGIA wrote: Hi again, I have the following: I have not changed anything in ffG53a6.atp and .rtp As suggested by gmx users, I have the following in the ions,itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge

Re: Re: Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread SHIVANGI NANGIA
Hi again, I have the following: I have not changed anything in ffG53a6.atp and .rtp As suggested by gmx users, I have the following in the ions,itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1

Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread Justin A. Lemkul
SHIVANGI NANGIA wrote: Hello, Thanks a lot for the suggestion. I think I made some progress but I am not there yet. I added the following in the ions.itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH

Re: Re: [gmx-users] Hydroixde Ion

2011-03-22 Thread SHIVANGI NANGIA
Hello, Thanks a lot for the suggestion. I think I made some progress but I am not there yet. I added the following in the ions.itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1 0 1 OW 1 OWOW 1 -

Re: [gmx-users] Hydroixde Ion

2011-03-21 Thread Mark Abraham
On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote: Hello, I am new gromacs user. I am trying to set up a water-methanol system with few hyrdroxide ions. Since hyrdroxide ion does not already exist in gromacs database, I defined the following in the .rtp file ( I am using ffG53a6) [ OH ] [ atoms