Re: [gmx-users] How to tell if the molecule is correctly reduced?

Thanks Roland and Mark for your input.I did pdb2gmx -ss and checked the top file where the Cys are represented as CYSH, but when I loaded the generated pdb file in vmd, I can still see the original dsulfides bond, and each sulfur is protonated. Is this an artifact? Is there another way to

[gmx-users] How to tell if the molecule is correctly reduced?

Hi I did simulations for a protein with disulfide bonds using opls. Then I reduced the ssbonds in vmd and did simulations for the reduced. When loading gro(or pdb) and trr files on vmd I do not see reduced bonds. I also compared the two pdb files and they looked the same in terms of number of

Re: [gmx-users] How to tell if the molecule is correctly reduced?

Hi, if the gro file written by pdb2gmx contains the same number of hydrogens then before, than you disulfide bonds haven't changed. pdb2gmx automatically forms disulfide bridges if the atoms are within some distance (see specbond). Look at the output of pdb2gmx and make sure it is doing what you

Re: [gmx-users] How to tell if the molecule is correctly reduced?

- Original Message - From: Roland Schulz rol...@utk.edu Date: Thursday, August 26, 2010 3:06 Subject: Re: [gmx-users] How to tell if the molecule is correctly reduced? To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, if the gro file written by pdb2gmx contains the same