Dear Sir
Please guide me the issue regarding PLP and Lysine. I have tried tutorial
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/ but i am
getting again error.
Kindly guide me for this issue.
Regards
Aashish
On Sat, Mar 3, 2018 at 5:05 PM, Aashish Bhatt <aashish.ph16221.inst.ac.in>
wrote:
> 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 Thu Mar 08 2018 - 07:00:03 PST
