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 : > On 29/04/2012 7:02 PM, Hagit G wrote: >> I'm trying to work on thrombin pdf file with 2 chains. The pdb co

Re: [gmx-users] disulfide bonds

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 atom

[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, but