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 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 I didn't make it because one Cys >> is in the long chain and the other one is in the short chain) > > See http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds > about requirements for having atoms (and thus chains) in the same > [moleculetype]. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
