Re: [AMBER] tleap PDB file in ORCA

From: David Cerutti <>
Date: Thu, 18 Jun 2020 04:18:50 -0400

Not sure if this would be of help, but have a look at the mdgx &configs
module. It will sample configurations using an Amber force field (prmtop)
and a series of restraints that you can use to literally play with your
small molecule. It will then produce any number of output structures,
sieving them for clashes and other sanity checks, and has the option of
printing ORCA input files with the resulting coordinates. It may not
produce exactly the ORCA calculation deck you want, but you could write a
short script to grep out that line and replace it with the calculation you
do want.


On Thu, Jun 18, 2020 at 3:23 AM Benedikt Flöser <>

> Dear all,
> I am trying to use PDB files generated by tleap in ORCA and noticed that
> has a problem assigning the correct elements because it can't process the
> third column containing this information correctly.
> My question now is: is there a reason why tleap does not print the element
> identity in a column at the end of each line like it is done in PDB files
> from
> the databank? I realized ORCA is looking for this column and not being
> able to
> find it, uses the information in the third column which leads to erroneous
> assignments.
> Best,
> Benedikt
> --
> Dr. Benedikt M. Flöser
> Max-Planck-Institut für chemische Energiekonversion
> Stiftstraße 34-36
> 45470 Mülheim a.d. Ruhr
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Received on Thu Jun 18 2020 - 01:30:03 PDT
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