Hi,
alternatively, you could use the crgmask functionality in sander, which
sets charges for a set of atoms to zero, e.g.
crgmask=":1.CA"
Thomas
On Wed, June 20, 2012 2:17 am, Daniel Sindhikara wrote:
> I just had this problem, I wrote a quick bash script. Make sure to check
> your new prmtop afterwards to make sure it looks correct.
> For my prmtop the next flag after CHARGE was ATOMIC_NUMBER. Not sure if
> this is always the case. I'm sure someone else
> has a more elegant way to do it.
>
>
> chargeline=`grep -n CHARGE my.prmtop | cut -f1 -d ":"`
> headendline=`expr $chargeline + 1`
> atomicnumberline=`grep -n ATOMIC_NUMBER my.prmtop | cut -f1 -d ":"`
> tailstartline=`expr $atomicnumberline - 1`
> head -n $headendline my.prmtop > prmhead
> sed -e "1,$tailstartline d" my.prmtop > prmtail
> echo $atomicnumberline
> numchargelines=`expr $atomicnumberline - $chargeline - 2`
> head -n $tailstartline my.prmtop | tail -n $numchargelines > charges
> for digit in 1 2 3 4 5 6 7 8 9
> do
> perl -pi.bak -e "s.$digit.0.g" charges
> done
> cat prmhead > my.prmtop
> cat charges >> my.prmtop
> cat prmtail >> my.prmtop
>
> -Dan
>
>
> On Wed, Jun 20, 2012 at 2:56 PM, Adam Jion <adamjion.yahoo.com> wrote:
>
>> Hi,
>>
>> Is there an easy way to temporarily switch-off the partial charges of my
>> molecules?
>> The very hard way (and only way?) is to modify the .prmtop file by hand.
>>
>> Regards,
>> Adam
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>>
>
>
>
> --
> Dr. Daniel J. Sindhikara <http://goo.gl/fLAqx>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/> - Biwako Kusatsu
> Campus <http://www.ritsumei.ac.jp/eng/html/about/abo_08.html/#kusatsu>
> sindhikara.gmail.com
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
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Received on Wed Jun 20 2012 - 01:00:03 PDT
