Hi Fernando,<br>
How big is your system or say the box size. How big is your protein?<br>
And is there any reason, why you want to add only 216 water molecules?<br>
<br>
if you use -ci option, make sure you have only one molecule in
water.gro file and use -nmol xxx to add xxx no. of water molecules, but
if you use -cs option, the number of water molecules added depends on
the box size as well as the protein inside the box. It adds water
molecules to solvate the protein.<br>
<br>
-Viswam.<br><br><div><span class="gmail_quote">On 11/8/05, <b class="gmail_sendername">Osmair Vital de Oliveira</b> <<a href="mailto:osmair@qt.dq.ufscar.br">osmair@qt.dq.ufscar.br</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>Hi Fernando<br><br>Using:<br>genbox -cp minimized_box.gro -ci spc216.gro -o<br>minimized_water3.gro -p aki.top<br><br>use too: -box x y z<br><br>Osmair V. Oliveira<br>UFSCar - SP - Brazil<br><br>On Tue, 8 Nov 2005, Fernando Mattio wrote:
<br><br>> 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<br>> molecules coordenates, and of course the
spc.itp file. I am trying to learn<br>> 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<br>> minimized_water3.gro -p
aki.top<br>> But I got the Fatal Error: more than 1 residue in insert molecules. Program<br>> terminated.<br>> I couldnīt understand this error.<br>><br>> I tried also : genbox -cp minimized_box.gro -ci spc216.gro
-o<br>> 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<br>> 1 molecule". What does it means, that I should add one by one the 256
<br>> molecules?<br>> Or shouldnīt I use genbox (and maybe work with the topologies files) for<br>> such a thing?<br>> Many thanks and best regards,<br>> Fernando Mattio.<br>><br>><br>> 2005/11/8, Dallas B. Warren <
<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</a>>:<br>> ><br>> > 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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</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br>