Re: [gmx-users] How to remove H atom from residue in gro file?

2012-05-03 Thread Hagit G
Ho THANKS MANY THANKS I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much. Hagit. 2012/5/2 Mark Abraham mark.abra...@anu.edu.au On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with

Re: [gmx-users] How to remove H atom from residue in gro file?

2012-05-02 Thread Justin A. Lemkul
On 5/2/12 6:55 AM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore

Re: [gmx-users] How to remove H atom from residue in gro file?

2012-05-02 Thread Mark Abraham
On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs

Re: [gmx-users] How to remove H atom from residue in gro file?

2008-01-18 Thread Nelson Cotrim
Hi Maik, Thanks for the warning and the tip, I have already donwloaded and will read that paper today, it seems to be what I need. I have been working with MD for some 6 months now (I know that's not much), and have had the help of some knowledgeable people, but they are unavailable right now. I

Re: [gmx-users] How to remove H atom from residue in gro file?

2008-01-18 Thread Justin A. Lemkul
Dear All, In working with Nelson on his problem (below), I made some headway into figuring out what is going on with the ffG43a1p force field files. I know a few others have asked questions about it across this list, so I thought I would send this out to everyone. By modifying a few entries in