Hi,
It seems to me that your ligand (lig.mol2) has some problem. If the net
charge of this molecule is not -1, then it should be a radical according to
chemists' intuition. What is the spin multiplicity when you did QM
calculation?
Best
Junmei
On Wed, Dec 9, 2009 at 6:16 AM, Jio M <jiomm.yahoo.com> wrote:
> Dear AMBER users;
>
>
>
> I am attaching files of ligand mol2 (lig.mol2) and its frcmod (lig.frcmod).
> and solvent mol2 (dcm.mol2) and frcmod as dcm.frcmod
>
>
>
> Now I tried with dynamics of single ligand with dcm solvent. I
> found that same problem of COOH atoms is occuring. I have used GAFF.
>
> I solvated like this (with single solvent molecule)
>
> solvateoct ligand dcm 10
>
> approx. 180 dcm were added.
>
>
>
> 1) Using prmtop and inpcrd file I minimised first with restraints on
> ligand only. It minimised without error as restraints were applied on
> solute so atoms of COOH did not trouble.
>
> 2) But after removing constraints, error came indicating atoms of COOH.
>
>
>
> 3) Then I tried directly NVP dynamics using rst file of restraint
> minimisation (1 step) and this input:
>
> &cntrl
>
> imin = 0,
>
> ntb = 2, pres0 = 1.0, ntp = 1,
>
> taup = 2.0,
>
> cut = 10.0, ntr = 0,
>
> tempi = 0.0, temp0 = 0.0,
>
> ntt = 3, gamma_ln = 1.0,
>
> nstlim = 100000, dt = 0.0001,
>
> ntpr = 100, ntwx = 100, ntwr = 1000
>
> /
>
>
>
> here I can see in trajectory that
>
> a) the hydrogen of COOH is approaching towards carbonyl oxygen of COOH.
>
>
>
> b) ALSO all the rings are distorted and I think rings are behaving as
> Cyclohexane.
>
>
>
> I think some parameters are missing? Please help and suggest which
> parameters I am missing here.
>
>
>
> thanks and regards;
>
> JIomm
>
>
>
>
>
>
>
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Received on Wed Dec 09 2009 - 15:30:03 PST
