Moeed wrote:
Dear Justin,
Actually, I used -d option because you said the atoms in the box must be
half a bond length from the edges of box...I thought maybe this can be
done by -d...
My point was that you should not be using a combination of -box, -d, and -angles
simultaneously. Use either -box or -d, not both, and don't use -angles.
With PRODRG I am unable to produce coordinate file a chain with less
than three C atoms.
I sketched the molecules:
C-C ethane
C=C Ethylene
but I am getting a message:
ERRDRG> PRODRG does not deal with mono/di-atomic molecules.
PRODRG> Program terminated unsuccessfully, sorry!
1- Could you please help me with this. (actually I need structure file
of ethylene in the future)
So make a 4-carbon repeat unit. It's easy to draw chains with PRODRG (but there
is a limitation to the number of atoms).
-Justin
2- How can I generate structure file of repeating unit -CH2-CH2- with
PRODRG. I tried the followings...and all I am getting is the above
message.. :(
H H
| |
C-C
| |
H H
H H
| |
-C-C-
| |
H H
-C-C-
Moeed
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
