Well, ffG43a2 is a GROMOS FF too! So look at the topology and you'll
see that
it also misses some NON_POLAR hydrogens. You probably generated you itp
file using pdb2gmx and got a gro file with it. Then the absence of H
did not
appear!
The H that are involved in H-bonding are explicitly rep
Anirban Ghosh wrote:
Hi XAvier,
Thanks for the reply. Actually I want to use this ligand with a protein
and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it
correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not
explicitly described? Because in protein-lig
Hi XAvier,
Thanks for the reply. Actually I want to use this ligand with a protein and
run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct
to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly
described? Because in protein-ligand complexes, hydrogen bond
You have the proper itp file for the GROMOS FF. Some H are not
explicitly
described!
On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote:
Hi, XAvier,
Sorry for that mistake. Yes, exactly PRODRG is not giving the non-
polar hydrogens. There I am using the GROMOS96.1 FF. So is there any
way
Hi, XAvier,
Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar
hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get
the proper .itp file? I mean any other online server like PRODRG? Or How can
I derive the proper .itp file manually?
Any suggestion is welco
You are missing HB1 and HB2, not HB2 and HB3 :))
This is due to the force field our are using. Gromos I presume: it
uses the united H idea: non-polar H are not explicitly modeled.
you should be able to erase those from your gro file, but I would
suggest you get into some literature about the FF
Hi ALL,
I have a ligand LDOPA with 25 atoms (including all hydrogens).:
---
DAH COORDS
25
1DAH O1 5.988 5.216 9.128
1DAH C2 5
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