Dear Thomas,
Many thanks for your kind email. Here is the content of my frcmod file:
This frcmod file is for ZNA (zinc 2+ ion)
MASS
ZNA 65.400
NONBON
ZNA 1.10 0.013
As you can see there is no parameter for bond angles and torsions in frcmod file. I would have thought that Zn2+ is going to be involved just in nonbonded interactions. I am assuming that Amber decides to create bonds between Zn and neighbouring atoms and asking for those parameters. Is there any work around for this problem?
Cheers,
Siavoush
On Tuesday, 7 March 2023, 03:03:05 pm GMT+3:30, Steinbrecher, Thomas via AMBER <amber.ambermd.org> wrote:
Hi Siavoush,
your leap output lists a few bond, angle and torsion parameters that are
missing, that is why it isn't saved. This is most likely due to atom name
mismatches somewhere. Could you check that your frcmod file contains the
parameters listed as missing, e.g. a bond for atom types O2-ZNA or an angle
term for CR-NB-ZNA? Since all missing parameters involve the ZNA atom, my
suspicion is that you have a different name for the Zn ion in the frcmod
file.
Kind Regards,
Thomas
On Tue, Mar 7, 2023 at 11:32 AM Siavoush Dastmalchi via AMBER <
amber.ambermd.org> wrote:
> Dear List,I have a zinc atom in my protein-ligand complex pdb file. I was
> trying to do same kind of calculations on the complex presented in tutorial
> 4b (https://ambermd.org/tutorials/basic/tutorial4b/). I prepared .lib and
> .frcmod files for zinc ion according to the instruction given kindly by
> Ross at
> https://structbio.vanderbilt.edu/archives/amber-archive/2004/4188.php.
> Unfortunately, I wasn't able to produce rst7 and prmtop files for the
> complex. Please see the attached file for the commands and messages I have
> got.I will appreciate you kind attention.Cheers,Siavoush
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Sat Mar 11 2023 - 00:00:03 PST
