[gmx-users] Re: EDO and TRS ligand
tsjerkw at gmail.com
Thu Apr 14 11:06:03 CEST 2011
Please refrain from sending personal e-mails, unless you're invited to do so.
> I am working on the EDO and TRS ligands for 2/3 weeks.But I dont solved it.
> Please help me.
This is what supervisors are for. I assume you have one.
> 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?
There will be symmetry on average, but that does not mean there is
symmetry at every instant, which is what you get from QM calculations.
> can you advice me the other program/software to calculate charge? please do
> not get angry. I do not know what to do. I'm so desperate.
No I can't. You should probably discuss with your supervisor.
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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