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-- Dr. Dean Cuebas, Associate Prof of Chemistry deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 > From: Junmei Wang <junmwang.gmail.com> > Reply-To: AMBER Mailing List <amber.ambermd.org> > Date: Wed, 9 Dec 2009 17:17:12 -0600 > To: AMBER Mailing List <amber.ambermd.org> > Subject: Re: [AMBER] Re: COOH troubling > > 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 >> >> >> >> >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Dec 09 2009 - 16:30:02 PST