abdullah ahmed wrote:
Hello gromacs users,
I have asked this question before but perhaps I was not clear enough. I
noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure
has some side chains located very close to each other then after energy
minimisation they become distorted (for example, Phe ring is not flat, and
for Leu some hydrogen atoms move away from the rest of the side chain).
I realize that these problems are probably due very close packing of the
sidechains in the initial structure.
But I hope to keep the close contacts in the initial structure and obtain
correct stereochemistry of the molecule after the minimisation. Is this
possible?
The outcome of energy minimization is dictated by the functional form of your
chosen force field and the parameters it assigns to the constituent atoms in
your structure. If you're getting unreasonable geometry after EM, then your
starting structure is physically unreasonable. You could try to restrain and/or
freeze these configurations, but I would suspect that any subsequent MD will
crash instantly when these atoms shear apart from one another. If the
configuration is not stable in EM, it will not be stable in MD.
-Justin
Sorry for bothering you again and thank you in advance for your help,
Abdullah Ahmed
--
========================================
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/Support/Mailing_Lists/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/Support/Mailing_Lists
