[gmx-users] Re: EDO and TRS ligand

[Tsjerk Wassenaar]

Ahmet,

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.
> 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?

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.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands