Иимяа Фаамиилиияа wrote:
Hi,
I am trying construct homopolymer from non-standard monomers .
I have pdb, itp and gro files for monomer and constructed pdb file for polymer.
I can put them in corresponding top/forcefield.ff directory.
But how I can get itp and gro files for polymer (for example, for 3-mer in
simplest case)?
How Gromacs knows which atoms are "head" and "tail" atoms for connection of monomers
into polymer (like in "Material Studio")?
The best approach is to build .rtp entries and have pdb2gmx build your topology
for you. That way, you can build polymers of any size you like. See the
instructions and linked example at:
http://www.gromacs.org/Documentation/How-tos/Polymers
-Justin
--
========================================
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
