Hi Dallas and gromacs users,<br>
I understood what you wrote, but I had problems...<br>
I have a protein in a box, and also one file (spc216.gro) with 256
water molecules coordenates, and of course the spc.itp file. I am
trying to learn how to add exactly these 256 molecules with itīs
coordenates in the box...<br>
I tried: genbox -cp minimized_box.gro -ci spc216.gro -nmol 256 -o minimized_water3.gro -p aki.top<br>
But I got the Fatal Error: more than 1 residue in insert molecules. Program terminated.<br>
I couldnīt understand this error.<br>
<br>
I tried also : genbox -cp minimized_box.gro -ci spc216.gro -o minimized_water3.gro -p aki.top<br>
And only 78 water molecules were added.<br>
<br>
I also read in the manual that "At the moment -ci only works when
inserting 1 molecule". What does it
means, that I should add one by one the 256 molecules?<br>
Or shouldnīt I use genbox (and maybe work with the topologies files) for such a thing? <br>
Many thanks and best regards,<br>
Fernando Mattio.<br>
<br><br><div><span class="gmail_quote">2005/11/8, Dallas B. Warren <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Because using the -cs switch tells it to fill the box up with as many of<br>those molecules as it can.<br><br>If you just want to add a limited number, you need to use the -ci switch<br>with -nmol<br><br>Catch ya,<br><br>
Dr. Dallas Warren<br>Lecturer<br>Department of Pharmaceutical Biology and Pharmacology<br>Victorian College of Pharmacy, Monash University<br>381 Royal Parade, Parkville VIC 3010<br><a href="mailto:dallas.warren@vcp.monash.edu.au">
dallas.warren@vcp.monash.edu.au</a><br>+61 3 9903 9073<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble<br>a nail.<br>_______________________________________________
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