On 14/04/2011 7:06 PM, Tsjerk Wassenaar wrote:
I am using the wavefunction spartan 8 program to calculate charges.
revised_EDO.itp
...
[ moleculetype ]
; Name nrexcl
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 EDO OAB 1 -0.530 15.9994
2 H 1 EDO HAE 1 0.332 1.0080
3 CH2 1 EDO CAA 1 0.198 14.0270
4 CH2 1 EDO CAC 2 0.198 14.0270
5 OA 1 EDO OAD 2 -0.530 15.9994
6 H 1 EDO HAF 2 0.332 1.0080
I didnt change dihedral angel, bond .... do I have to change them? I didnt
arranged for (COH)3(NH3+)C to have charges consistent with its symmetry (TRS
ligand). I have different charge for CH2 groups, H, O. That is, There is not
symmetry. What should I do?
An solvated TRS will be best modeled with the same set of partial
charges on each symmetric side group (e.g. COH). So every oxygen atom
should have the same partial charge. To do this, generate a structure of
this compound that has the three-fold symmetry so that whatever
technique you use to generate charges will do so symmetrically. Then,
test them extensively against experimental data.
When bound as a ligand, those charges might differ between
ostensibly-equivalent atoms, but trying to parametrize the charges in
the context of the binding site is outside your scope at this time.
Mark
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
