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 - 07:00:02 PDT
