[gmx-users] zero SOL molecules

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 6 13:31:21 CET 2011

sarah k wrote:
> Dear all,
> I am adding Nitrogen box instead of water molecules to my protein. Based 
> on your guidelines I generated the coordination and topology file of 
> nitrogen. Then I used the following command:
> genbox -cp A_newbox -ci -42000mol N2C.gro -o A_solv.gro -p topol.top
> N2C.gro is my new file made manually whithin all information in 
> spc216.gro. I replaced all data in spc216.gro with N2C but I kept the 
> name unchanged:
> genbox -cp A_newbox -ci -42000mol N2Cspc216.gro -o A_solv.gro -p topol.top
> The box was generated but there were 0 SOL molecules. The error is: 
> Invalid command argument: spc216.gro

I sincerely doubt that a box was generated if you get a fatal error about an 
invalid argument.  One would also expect that you will have 0 SOL molecules, 
since you're not actually dealing with water, are you?

> How can I fix it? Thanks. 

Use a sensible command.  "-42000mol N2Cspc216.gro" is where the problem is. 
Option -ci takes a coordinate file containing *one* molecule to be inserted, and 
-nmol tells genbox how many of them to insert.  Messing with spc216.gro is both 
confusing and unnecessary.


> Best regards,
> Sarah Keshavarz 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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