Re: [AMBER] Problem in creating topology of NAD

From: Ashutosh Shandilya <>
Date: Fri, 2 Mar 2012 12:25:25 +0530

Loading Prep file: ./nadDRG.prepin
Loading parameters: ./naddrg.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading library: ./nad.lib
Loading PDB file: ./nad.pdb
  total atoms in file: 70
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
WARNING: The perturbed charge: -1.000000 is not zero.

prepin, frcmod library and pdb file is with the attachment.

On 2 March 2012 12:20, Ashutosh Shandilya <> wrote:

> Dear all
> 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.
> Thanks and regards
> Ashutosh Shandilya

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Received on Thu Mar 01 2012 - 23:00:02 PST
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