On 12/12/12 6:54 AM, James Starlight wrote:
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups.
As I've posted above my initial model was CAPPED from C and N termi by
NH2 and Ace. The resulted topology consisted of Improper for bonds
between chromophore atoms and Capped groups ( e.g :
With ACE (C-3 O-1 C-4 H-11 H-12 H-1 )
IMPH C N1 CA3 O
IMPH N C3 CA1 H11
IMPH C3 O1 N C4
IMPH C4 HC11 C3 H1
IMPH C4 HC11 C3 H12
With NH2 (N1-H2-H3)
IMPH N1 H2 C H3
IMPH C N1 CA3 O
That strings were removed from chromophore RTP. But in my final model
there are 2 amino acids insted of capped groups so the IPROPERS must
be inclusion for protein-chromophore nonds. How it could be done ?
In some amino acids I've found -N and -C blocks that (if I understood
correctly) for C and N atoms of the adjacent residues. How that atoms
must be defined correctly in the protein-chromophore comples ?
+ and - indicate next and previous residues, respectively. Presumably your
chromophore engages in the same types of peptide bonds as any other amino acid,
so the syntax is the same as any other case.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
