Maybe this previous post will be of some use:
http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html
-Justin
Alexander Bujotzek wrote:
Dear all,
I am experiencing some trouble with a small molecule containing a C-C
triple bond, using a topology built by PRODRG beta. I intend to use
ffG43a2, with a contraint on all bond lengths.
Energy minization does not converge, as forces on the atoms involved in
the bond seem to oscillate (not very high forces, though).
Position restrained MD fails with LINCS errors,
and unrestrained MD leads to a blow-up of the system.
I guess the fault lies in the representation of the triple bond in the
topology file, as a derivate of the molecule (with a single bond in the
same place) works just fine.
Excerpt from the itp building block provided by PRODRG beta. The triple
bond is supposed to be between carbons 18 and 19:
[ bonds ]
...
17 18 2 0.147 3422818.4 0.147 3422818.4 ; CAQ CAR 18
19 2 0.122 2309822.8 0.122 2309822.8 ; CAR CAS 20 19
2 0.147 3422818.4 0.147 3422818.4 ; CAT CAS
...
[ angles ]
...
16 17 18 2 109.5 520.0 109.5 520.0 ; OAP CAQ
CAR
17 18 19 2 180.0 41840001.2 180.0 41840001.2 ; CAQ CAR
CAS
18 19 20 2 180.0 41840001.2 180.0 41840001.2 ; CAR CAS
CAT
19 20 21 2 109.5 520.0 109.5 520.0 ; CAS CAT
OAU
...
There is no dihedral with 18 and 19 in the middle, but I assume that is
correct as triple bonds are not supposed to be "rotatable"?
What strikes me is the high force constant on the two 180 degree angles...
may that be a source of error?
Any help is appreciated! Maybe someone even has a working template of a
correct triple bond topology at hand?
Best regards and thank you for reading
Alex
PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C
triple bond... or maybe it's just the heat in my office.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
