<div><FONT size=1>Thanks Mark,<BR>but your first answer didn't help me at all. I want to create pdb<BR> manually which will work with gromacs pdb2gmx comand in order to get gro<BR> and top using OPLS, and seeking for some clues. It doesn't matter if it<BR> is Hyperchem or JME or MOL, I need a proper pdb which will be<BR> understandable to Gromacs.<BR> <BR> I know that PRODGR is not compatible with OPLS, that's why I am<BR> asking how to change gro and top to enable them to be compatible with OPLS<BR> <BR> The same story and with beta files (with ff43a1.itp)<BR> <BR> I'm trying to run MD using OPLS with my own molecule solved in the<BR> water, for that I was trying to create mymolecule.itp database file, and<BR> in order to do so I need to know how to describe correctly dihedrals (in<BR> OPLS standart)<BR> <BR> 'what indicates?' it's just simple logic if I use edited on Windows<BR> files to produce new
gro and updated top files on <SPAN class=yshortcuts id=lw_1200483365_51 style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">Unix</SPAN>, that indicates to<BR> me that cpp have no errors in reading these files (may be I am wrong,<BR> because I do not know how these files are processed during each of these<BR> precesses - like genbox and editconf, probably it's different from<BR> grompp?).<BR> <BR> number of molecules of whater in top x3+1(my molecule)xn(number of<BR> atoms in that molec.)=total nr of atoms in gro file. (it would be in gro let's say 1500 atoms, and in top let's say DGR=1 and SOL=490).</FONT></div> <div><FONT size=1></FONT> </div> <div><FONT size=1>I know exist some short instructions how to do so, but I couldn't find them in the manual.</FONT></div> <div><FONT size=1>P.S.these links provided are pointing to the empty sites.<BR><BR></div></FONT><p> 
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