<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Dear Justin,</DIV>
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<DIV>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 ? </DIV>
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<DIV>Sincerely<BR></DIV>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Justin A. Lemkul <jalemkul@vt.edu><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <gmx-users@gromacs.org><BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Friday, March 13, 2009 8:25:14 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] using more than one type of molecules<BR></FONT><BR><BR><BR>Molecular Dynamics wrote:<BR>> <BR>> <BR>> Dear All,<BR>> <BR>> <BR>> 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 <BR><BR>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.<BR><BR>Use editconf to set your box size, and genbox -ci -nmol to insert what you need.<BR><BR>> 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 <BR><BR>If these come from PRODRG, they will probably require manual modification and validation of their contents.<BR><BR>> work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command<BR>> <BR>> <BR>> genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top<BR>> <BR>> <BR><BR>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).<BR><BR>> After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of
Y molecule and go on ..<BR>> <BR><BR>Correct.<BR><BR>-Justin<BR><BR>> <BR>> Could you please help me to learn the true process of using more than one type of molecules in gromacs ?<BR>> <BR>> <BR>> <BR>> Sincerely<BR>> <BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Graduate Research Assistant<BR>ICTAS Doctoral Scholar<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]<A href="http://vt.edu/" target=_blank>vt.edu</A> | (540) 231-9080<BR>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR><BR>========================================<BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www
interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR></DIV></DIV></div><br>
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