[gmx-users] Re: EDO and TRS ligand
Mark.Abraham at anu.edu.au
Thu Apr 14 12:43:02 CEST 2011
On 14/04/2011 7:06 PM, Tsjerk Wassenaar wrote:
>> I am using the wavefunction spartan 8 program to calculate charges.
>> [ 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.
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