Ashutosh Shandilya,
> 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.
> Thanks
I quickly looked at your frcmd file:
- add the missing dihedral in the DIHE section
- avoid duplicates such as N*-CA in the BOND section
- decide if you use capital (or non-capital letters) for atom types
See for instance
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff
regards, Francois
> On 2 March 2012 12:20, Ashutosh Shandilya <izerokelvin.gmail.com> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 01 2012 - 23:30:02 PST
