[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.
-Justin
> Best regards,
> Sarah Keshavarz
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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