subject:"Re\: \[gmx\-users\] disulfide bonds"

Re: [gmx-users] disulfide bonds

2012-04-29 Thread Mark Abraham

On 29/04/2012 7:02 PM, Hagit G wrote: 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

Re: [gmx-users] disulfide bonds

2012-04-29 Thread Hagit G

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