Marzinek, Jan wrote:
Dear Gromacs Users,
I used PRODRG server in order to obtain the topology file for my
molecule (52 atoms with all hydrogens). However, server generated
Gromacs topology which involves 47 atoms (for PDB file with
polar/aromatic hydrogens). Whether I will use the pdb file with missing
4 hydrogen that wont be a good apporximation. How to overcome this?
The Gromos96 force fields are united-atom force fields and may not use all the H
atoms your input coordinates did. If you suspect some issue with protonation
state, PRODRG can be forced into certain protonation with the ADDHYD or DELHYD
keywords. Be advised, of course, of the usual caveats regarding the quality of
PRODRG topologies:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-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
