[gmx-users] genbox give coord file more waters than top file

Erik Marklund erikm at xray.bmc.uu.se
Thu Mar 8 09:35:18 CET 2007

8 mar 2007 kl. 01.32 skrev Mark Abraham:

>> Dear gromacs guys
>> Why would genbox put more water molecules in my .gro file than in  
>> my .top
>> file? I'm sure all I have to do is edit the number in my top file,  
>> but I
>> have not had this happen before, does anyone know of  a reason  
>> that this
>> happens so I can fix my file?
> genbox doesn't read a top and produce that many solvent molecules.  
> For a
> start, how does it know what shape you want them in? Read "man  
> genbox",
> choose what you want to do, apply genbox, and then edit your .top  
> so the
> number of waters agrees with what genbox produced... not the other way
> around.
> Mark

I'm not so sure about that. genbox *does* take a top file as an  
optional argument. genbox -h tells me:

"Finally, genbox will optionally remove lines from your topology file  
in which
a number of solvent molecules is already added, and adds a line with the
total number of solvent molecules in your coordinate file."

I have never used this option, so I don't know exactly how it works,  
but I expect it to do what William wants it to do.

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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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