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 confirm that the molecule is properly reduced
Rabab Toubar --- On Wed, 8/25/10, Mark Abraham <[email protected]> wrote: From: Mark Abraham <[email protected]> Subject: Re: [gmx-users] How to tell if the molecule is correctly reduced? To: "Discussion list for GROMACS users" <[email protected]> Date: Wednesday, August 25, 2010, 8:57 PM ----- Original Message ----- From: Roland Schulz <[email protected]> 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 <[email protected]> > 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 expect/want. > > Roland > > On Wed, Aug 25, 2010 at 12:44 PM, Rabab Toubar <[email protected]> wrote: > 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 hydrogens in > cysteines. So how can I tell if the molecule is properly reduced before going > further. It can't be "properly reduced" by VMD. The coordinates and the topology both have to change, and VMD neither reads or writes .tpr and .top. Instead, use pdb2gmx -ss to allow you to choose which disulfides are made in the first place. Mark -----Inline Attachment Follows----- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
