for more features like angle or dihedral, merge each section of their
itp (offset all the numbers in the second itp for an offset) shall be a
more elegant way.
On 11/7/2007 6:00 AM, Tanping Li wrote:
Dear Yang,
Really thanks for the help. Distance constraint can
describe the bond length between ligand and protein,
how about other propery of covalent bond? Maybe I
missed something of your message.
Yours
Tanping
--- Yang Ye <[EMAIL PROTECTED]> wrote:
you might want to try distance constraint.
On 11/7/2007 5:11 AM, Tanping Li wrote:
Dear all,
I searched the mailling list, and still can't find
a
way to set up my system: a ligand covalently bond
to
protein.
I don't know if there is a easier way to do this.
What
I can think of is:
1) Add a bond I like in the specbond.dat file;
2) Add a block for ligand in the rtp file;
3) run pdb2gmx, gromacs will treat protein and
ligand
a one chain since it can see the bond in the
specbond.dat.
I just wonder if there is a eaiser way to add a
ligand
to rtp file? When I run Dundee PRODRG2, I get a
.itp
file. Is there some way to change this into rtp
format? It is not trival to write a rtp manually.
Really appretiate your help.
Yours
Tanping
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