Hi Joe,
The parameter files are in frcmod files rather than dat files. They're in
$AMBERHOME/dat/leap/parm/frcmod.phosaa14SB and frcmod.phosaa19SB
Lauren Raguette
Simmerling Lab | Stony Brook University
> From: Fernandez, Joseph P. <fernandez.99.buckeyemail.osu.edu>
> Date: Wed, Apr 14, 2021 at 9:45 AM
> Subject: [AMBER] Nonstandard Residue
> To: amber.ambermd.org <amber.ambermd.org>
>
>
> Hello Amber Community,
>
> I currently use the approach outlined in tutorial 5.3 (
> https://ambermd.org/tutorials/basic/tutorial5/index.php) to create non
> standard residues for my system of interest. The non-standard residues are
> phosphylated serines.
>
> I know there are libraries (phosaa10 and phosaa14SB) for phosphylated
> serines (SEP, S1P), but these residues do not have alkyl groups on the
> phosphate, which are necessary for my model.
>
> In the nonstandard residue preparation, parameters are taken from the
> $AMBERHOME/dat/leap/parm/parm10.dat file using parmchk2. I was hoping to
> borrow parameters from the phosaa set, but I cannot find the relevant file.
> Is there a .dat file for phosaa14SB? I cannot locate it within the
> directory.
>
> Many thanks for your help and time,
>
> Joe
> Joseph Fernandez
> Graduate Associate PhD Candidate
> The Ohio State University
> Hadad Research Group Department of Chemistry and Biochemistry
> 410 CBEC, 151 W Woodruff Ave, Columbus, OH 43210
> 440-429-2220 Mobile
> fernandez.99.osu.edu<mailto:fernandez.99.osu.edu> / osu.edu<http://osu.edu
> >
>
>
>
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Received on Wed Apr 14 2021 - 08:30:02 PDT
