AMBER Archive (2009)

Subject: [AMBER] Re: COOH group trouble

From: Jio M (jiomm_at_yahoo.com)
Date: Wed Dec 09 2009 - 10:38:09 CST

Dear Sir,

I have tried dynamics on acetic acid.

Same, I optimised with HF/6-31G* and then esp calc. After RESP
derivisation of charges with antechamber.I can run minimisation and
dynamics successfully. Trajectory shows

normal behaviour of COOH..

 I used same input files( of acetic acid minimisation ) for my
ligand dynamics also. Again  ********* error indicating of
carboxylic acid atoms.

here is min1 input (same for acetic acid and ligand dynamics in dcm):

initial minimization solvent DCM

 &cntrl

  imin   = 1,

  maxcyc = 2000,

  ncyc   = 1000,

  ntb    = 1,

  ntr    = 1,

  cut    = 8.0

  ntc = 2, ntf = 2

 /

hold

500.0

RES 1 3

END

END

below is my min2:(same for both dynamics)

whole system

 &cntrl

  imin   = 1,

  maxcyc = 2000,

  ncyc   = 1000,

  ntb    = 1,

  cut    = 8.0

 /

Please help to sort it out

thanks and regards;

JIomm

      
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