Dear Amber mailing list,
I am using xparmed.py to output a list of all the dihedrals in a glycoprotein model I built using the GLYCAM glycoprotein builder tool. I start the xparmed program and execute these commands:
xparmed.py
choose the glycoprotein prmtop file (generated by tleap)
click printDihedrals and choose all the atoms of the protein in the mask
The list of dihedrals generated however, mention some strange atom names that are not originally present in the protein structure pdb file e.g 3C
16 C ( C) 18 N ( N) 20 CA ( CX) 22 CB ( 3C) 2.0000 1.0000 0.0000 1.2000 2.0000
M 16 C ( C) 18 N ( N) 20 CA ( CX) 22 CB ( 3C) 1.8000 2.0000 0.0000 1.2000 2.0000
M 16 C ( C) 18 N ( N) 20 CA ( CX) 22 CB ( 3C) 0.8000 3.0000 0.0000 1.2000 2.0000
M 16 C ( C) 18 N ( N) 20 CA ( CX) 22 CB ( 3C) 0.0000 4.0000 0.0000 1.2000 2.0000
It therefore also outputs dihedrals defined by the same 4 atoms. Looking back at the prmtop file for the protein, the atoms are defined like this:
N H1 H2 H3 CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA
HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3
OG HG C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C
Is it possible there is a bug in the xparmed.py program that results in splitting the columns of the prmtop file such that the program thinks there are atom types that don't really exists e.g 3C and 2C? Is this why there are multiple dihedrals generated for the same 4 atoms?
Thanks,
Nathalie
P.s attached is the prmtop file of the glycoprotein
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Received on Tue Dec 08 2015 - 07:30:03 PST
