Re: [AMBER] Problem in creating topology of NAD

From: FyD <>
Date: Fri, 02 Mar 2012 08:05:26 +0100

Dear Ashutosh Shandilya,

> I am trying to make topology file for NAD atom. I downloaded the
> coordinates of NAD from RCSB and made the library file and added missing
> parameteres in the frcmod file. But it could still not save the topology
> file for NAD while building H bond parameters.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> ** No torsion terms for CA-CA-N*-CA
> ** No torsion terms for CA-N*-CA-CA
> ** No torsion terms for CT-N*-CA-CA
> ** No torsion terms for CT-N*-CA-CA
> Building improper torsion parameters.
> total 3 improper torsions applied
> *Building H-Bond parameters*.
> *Parameter file was not saved.*
> I have tried various combination and any help is appreciated or if any
> information is missing let me know.

You need to provide two dihedral force field parameters in your frcmod file...
i.e. for CA-CA-N*-CA and CT-N*-CA-CA

or you can try NAD from R.E.DD.B.

get F-90.tar.bz2 for instance

tar jxvf F-90.tar.bz2
cd F-90
perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
tleap -f script1-new.ff

See also in case you want to generate the prmtop/prmcrd files:
perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1.ff
  or may be adapt it:
perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1-new.ff

regards, Francois

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Received on Thu Mar 01 2012 - 23:30:01 PST
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