Hi Chris,
Could you please try applying the attached patch. Copy it to
$AMBERHOME/src/sander/
cd $AMBERHOME/src/sander
patch -p0 <bugfix.19
make clean
make sander
mv sander ../../exe/
cd ../../test/
make test.serial.QMMM
Then let me know if it works for your system and I'll post it as a bugfix on
the AMBER website.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of C Liu
> Sent: Saturday, May 02, 2009 7:09 PM
> To: amber.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
>
>
>
>
- application/octet-stream attachment: bugfix.19
Received on Wed May 20 2009 - 15:08:48 PDT
