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

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

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

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 it because *each cystein is on a

[gmx-users] disulfide bonds

I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after,

Re: [gmx-users] disulfide bonds

thank you very much That was what I've tried to use pdb2gmx-ss, this is not useful, 'cause it's not in the same unit. My problem is not the distance. Hagit 2012/4/29, Mark Abraham mark.abra...@anu.edu.au: On 29/04/2012 7:02 PM, Hagit G wrote: I'm trying to work on thrombin pdf file with 2