Hi Alex,
Thanks a lot for replying.
I think I understand what you are saying. I think the difference between the issues you had and the problem that I am having is that antechamber does recognize the correct atom types (I checked in leaprc.gaff and gaff.dat). So I have the correct atom definitions in the frcmod files, but they just get combined at the LEAP stage. I think manually changing the final topology file to reflect the correct atom types/ parameters is going to be my last resort.
Thanks for the heads up about the sp2 geometry though! I will make sure to keep an eye on the improper torsion angles when I build my topology files.
Thanks,
Govind Hegde
Postdoctoral Research Associate
Chemical & Biological Engineering Department
Colorado School of Mines
________________________________________
From: Alexander Martin Spring-Connell [aspring1.gsu.edu]
Sent: Tuesday, June 20, 2017 4:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] LEAP Merging Atom Types
I meant to clarify what I meant by “alter the frcmod file.” I went through the gaff definitions file and searched for the atom types, bonds, angles, and torsion angle definitions for the atoms it should have chosen then substituted those back into the frcmod file to replace the incorrect definitions. Also, you should pay attention to the improper torsion angles it selects to insure that sp2 geometry has been conserved. For my system, Antechamber ignored sp2 geometries; this became apparent in the first minimization.
I rebuilt the fragment multiple times in different software packages and different file formats. Each gave me identical results in Antechamber. Manually modifying the frcmod file was my only solution.
Again, this was all done several years ago on a rather old version of Amber. Hope this helps.
Alex
On 6/20/17, 6:14 PM, "Alexander Martin Spring-Connell" <aspring1.gsu.edu> wrote:
I’ve had similar issues with gaff on a unique nucleobase; improper gaff atom types were chosen which then loads incorrect distance, angle, and torsion angle definitions into the frcmod file. The only solution I could find was to manually inspect and alter the frcmod file. Note, I was using a rather old version of Amber (either 8 or 9).
Not the best solution, but it worked for me in the end.
Alex
On 6/20/17, 5:10 PM, "Govind Hegde" <ghegde.mines.edu> wrote:
Dear Amber Members,
I am trying to set up a system in LEAP containing 3 molecule types: small graphene sheets, a perfluorocarbon and water. I am currently using GAFF, and my graphene sheets have two atom types ( ca and ha) and the PFC's have 6 atom types (oh, ho, o, c, c3 and f). However, when I use LEAP to set up my topology file, I see that LEAP ignores the "c" in the PFC and merges that atom type with the "ca" in graphene, even though these two atom types have pretty different parameters in gaff.dat. Has anyone else experienced such a problem, and if so, is there a way to get around it? I have tried using both mol2 files as well as prep files to import the graphene and PFC units, with the same result.
Thanks for your help!
Best regards,
Govind Hegde
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Received on Wed Jun 21 2017 - 09:30:02 PDT
