AMBER Archive (2009)

Subject: [AMBER] Re: COOH troubling

From: Jio M (jiomm_at_yahoo.com)
Date: Wed Dec 09 2009 - 06:16:17 CST

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


  • application/octet-stream attachment: lig.mol2


  • application/octet-stream attachment: dcm.mol2


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