Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ?
Sincerely ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, March 13, 2009 8:25:14 PM Subject: Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: > > > Dear All, > > > I'm new to Gromacs and have some questions to learn the answers. I study on > one type molecule. If I want to add lets say 240 molecules, which is the best > way to use editconf or genbox ? And I learned the procedure of using more > than one type of molecules in gromacs. But I'm not sure, so I'm waiting for > your contributions. Assume that I have two small organic In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule. Use editconf to set your box size, and genbox -ci -nmol to insert what you need. > molecules like hydrocarbons X and Y. I think First I will have to get > seperately DRGGMX.ITP and DRGPOH..PDB for the each molecules in different If these come from PRODRG, they will probably require manual modification and validation of their contents. > work directories. Then chose one directory ( X ) and do the operations like > in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command > > > genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top > > If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water). > After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the > number of Y molecule and go on .. > Correct. -Justin > > Could you please help me to learn the true process of using more than one > type of molecules in gromacs ? > > > > Sincerely > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
