Dear Sir/Ma'am
In my protein lysine is covalently bound with PLP. I have tried preparation
of force field parameter of plp with lysine.
I am summarizing the steps that I have followed to create force field:
1. Extracted coordinate PLP and Lysine from protein and completed the
structure via attaching the Hydrogen.
Command used: *antechamber -i lys_plp.pdb -fi pdb -o lys_plp.prep -fo
prepi -c bcc -at amber -pf y*
*2. U*sed a parmchk2 command
*parmchk2 -i lys_plp.prep -o lys_plp.frcmod -f prepi -s 2*
In frcmod file,*I have not seen ATTN*
*3.*Without protein, parameter file prmtop and inpcrd created.
tleap
source leaprc.ff14SB.redq
source leaprc.gaff2
loadamberprep lys_plp.prep
loadamberparams lys_prep.frcmod
LYM=loadpdb lys_plp.pdb
saveamberparm LYM lym.prmtop lym.inpcrd
savepdb LYM lym.pdb
quit
But when I used protein with LYM(LYS+PLP)
tleap
source leaprc.ff14SB.redq
source leaprc.gaff2
loadamberprep lys_plp.prep
loadamberparams lys_prep.frcmod
LYM=loadpdb protein.pdb
check LYM
Checking parameters for unit 'lym'.
Checking for bond parameters.
Could not find bond parameter for: OH - N
Checking for angle parameters.
Could not find angle parameter: C - O - C
Could not find angle parameter: HO - OH - N
Could not find angle parameter: OH - N - H
Could not find angle parameter: OH - N - CX
Could not find angle parameter: P - OH - N
There are missing parameters.
My problem is with 'N' and which is a part of the peptide bond connected by
'C' and 'H' but, in the above error I am getting *N-OH instead of N-H*.
I kindly request you to help me find my mistake if any of the above steps.
I am attaching .prep and .frcmod file with this email for your further
reference. Please find the attachment.
Looking forward to your reply.
Regards
Aashish Bhatt
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Received on Sat Mar 03 2018 - 04:00:03 PST
