So, from the explanation made within table I understood that after selecting -ss option, I would see the type of cys as CYS2 in the constructed .gro file as well as in the .top file since the CYS2 name appears in the 8 th and 9 th columns and they are described as the new name for residue A and residue B.
So, I should perform a preliminary simulation in order to make the corresponding cysteine residue within the cutoff? -----Original Message----- From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Mon, 3 Mar 2008 20:46:15 +1100 (EST) Subject: Re: Re: [gmx-users] procedure for creating an S-S bridge > Thank you Mark, but I am a little bit confused. > > In the link you sent to me, > http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is > described in the specbond.dat file (in the first line). However, the > following sentence is written under the given table: > > "To describe new possible special bonds, such as disulfides, so that > pdb2gmx can generate them for you, you should add new lines similar to > these example lines, and update the counter in the first line. " > > So, I understood that the description made within the table does not > describe the Cys-Cys bond. Then, what does it represent? What do you think the second line of the file describes? > After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH > in the .gro file. ... and the pdb2gmx output doesn't report making a special bond, and using pdb2gmx without the -ss option produces the same output. Your conclusion here is...? > So, which one is true? > > Additionaly, I think, this type of information is not enough to create a > disulphide bond. My cysteine residues are not directed to each other for > making a Cys-Cys bond. So, what types of steps do I have to follow ? There > are papers, of course, in which these types of bonds are made, but the > description is not made properly. See the final line of the specbond.dat page. You'll need to change your input structure. Think about distance restraints and a preparatory MD simulation. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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