AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM assigns Cd to C, Se to S

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat May 02 2009 - 23:45:41 CDT

Hi Chris,

My apologies for this, it seems the code to identify atom types cannot
currently deal with Cadmium or Selenium (although of course it should).
These really are elements that are not extensively used hence why the
problem has slipped through the cracks.

I will add it to my task list for Monday and will send you a bugfix that
addresses it shortly.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of C Liu
> Sent: Saturday, May 02, 2009 7:09 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] QM/MM assigns Cd to C, Se to S
>
> Dear Amber Users:
>
> I am using the QM/MM interace, via the &qmmm namelist, to do a PM3
> calculation on a dimer that contains one cadmium and one selenium.
>
> 1. In tleap, the molecule is constructed as one unit containing one
> residue, from the pdb file:
>
> cdse=loadpdb cdse.pdb
>
> 2a. To make tleap write the prmtop and inpcrd files, I specified the
> type using the commands:
>
> set cdse.0.1 type Se
> set cdse.0.2 type Cd
>
> 2b. I typed "desc cdse.0.1", and I get:
>
> ATOM
> Name: Se
> Type: Se
> Charge: -0.6000
> Polarization: 0.0000
> Element: Se
>
> So tleap recognizes the elements
>
> 2c. I loaded the parameters file "cdse.frcmod". It contains dummy
> values, but I don't think this matters.
>
> loadamberparams cdse.frcmod
>
> The exact commands I typed are contained in the attachment "leap.in".
> The topology and coordinates files are in "cdse.prmtop" and
> "cdse.inpcrd".
>
> 4. I run a minimization with the options:
>
> &cntrl
> imin=1, maxcyc=500, ncyc=200, cut=12.0, ntb=0, ntc=1, ntf=1,
> ifqnt=1
> /
> &qmmm
> qmmask=':1', qmcharge=0, qm_theory='PM3',
> /
>
> 5. QM/MM assigns 'C' instead of 'Cd' and 'S' instead of 'Se':
>
> QMMM: QM Region Cartesian Coordinates (*=link atom)
> QMMM: QM_NO. MM_NO. ATOM X Y Z
> QMMM: 1 1 S 1.4800 2.4250 1.5280
> QMMM: 2 2 C -1.1160 2.0420 1.2060
>
> I can't find the documentation to guide me. I encounter the same
> issue when the molecule contains both QM and MM atoms.
>
> Chris Liu
>
>
>
>

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