[AMBER] How to add gaff parameters to PARMCHK.DAT file

From: Jiaan Zhu via AMBER <amber.ambermd.org>
Date: Thu, 6 Oct 2022 17:35:49 +0100

Dear Amber Users!

I’m trying to parametrize a nucleotide analog(named 1W5 in PDB), and when I run the following parmchk2 command ' parmchk -i 1w5.prepin -f prepi -o frcmod.1w5 -a Y -p dat/leap/parm/parm10.dat', it raised an error 'Atom type of NO does not shown up in PARMCHK.DAT’. I saw in AMBER Archive https://structbio.vanderbilt.edu/archives/amber-archive/2006/2734.php <https://structbio.vanderbilt.edu/archives/amber-archive/2006/2734.php> , there seems a way to get a combined parm99/gaff parameter file. I’m wondering if it is possible to add gaff parameters to PARMCHK.DAT file by a similar way and how to do that.

I already saw the David’s response for a similar problem http://archive.ambermd.org/202109/0177.html <http://archive.ambermd.org/202109/0177.html> , but not sure how to manually prepare the frcmod file by hand ab initio.

Many thanks!

Best regards,
Jiaan

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Received on Thu Oct 06 2022 - 10:00:02 PDT