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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