Dear Sir
I have sort out this issue. Problem was in plp.mc file but now i am facing
a new issue.
PLP bound with lysine, plp(C==N)Lys. If i used bond command, parameter is
not found of nitrogen.
If i am not giving bond command then it creates topology file without
forming bond between PLP and Lysine.
can you suggest how to solve the issue ?
Regards
Aashish
On Mon, Feb 12, 2018 at 7:16 PM, Aashish Bhatt <aashish.ph16221.inst.ac.in>
wrote:
> Dear Sir
>
> I am trying to prepare force field parameter of *PLP* (pyridoxal 5
> phosphate) and i have followed the tutorial http://ambermd.org/tu
> torials/basic/tutorial5/index.htm
> In my protein, PLP is covalently bound with Lysine(schiff base).
> I have used plp.cif file from pdb database.
>
> I used the following commands:
> 1. *antechamber -fi ccif -i PLP.cif -bk PLP -fo ac -o plp.ac
> <http://plp.ac> -c bcc -at amber*
>
> 2. In this step i prepared PLP.mc file. in pdb structure only C4A is
> head_NAME atom.
> when i used
>
> *prepgen -i plp.ac <http://plp.ac> -o plp.prepin -m plp.mc <http://plp.mc>
> -rn PLP*
>
> i got following warnings
>
> Warning: ATOM C3 has unfilled valence, assuming the linked atom name (in
> other residue) is "M"
> change "M" to "-M" if ATOM C3 is linked to the immediate previous
> residue
> change "M" to "+M" if ATOM C3 is linked to the immediate after
> residue
> Warning: ATOM C2 has unfilled valence, assuming the linked atom name (in
> other residue) is "M"
> change "M" to "-M" if ATOM C2 is linked to the immediate previous
> residue
> change "M" to "+M" if ATOM C2 is linked to the immediate after
> residue
> Warning: ATOM C2 has unfilled valence, assuming the linked atom name (in
> other residue) is "M"
> change "M" to "-M" if ATOM C2 is linked to the immediate previous
> residue
> change "M" to "+M" if ATOM C2 is linked to the immediate after
> residue
> Warning: ATOM C6 has unfilled valence, assuming the linked atom name (in
> other residue) is "M"
> change "M" to "-M" if ATOM C6 is linked to the immediate previous
> residue
> change "M" to "+M" if ATOM C6 is linked to the immediate after
> residue[
>
> 3. *parmchk2 -i plp.prepin -f prepi -o frcmod.plp -a Y \ -p
> $AMBERHOME/dat/leap/parm/parm10.dat*
> i got ATTN in
> i have follow line
> *grep -v "ATTN" frcmod.plp > frcmod1.plp*
>
>
>
> *parmchk2 -i plp.prepin -f prepi -o frcmod2.plp*
>
>
> *after this step i got the same error as was in plp.frcmod file (ATTN,
> need revision) *
>
>
> *Did i do any mistake in previous step ?*
>
> *Regards*
>
> *Aashish*
>
> *INST-Mohali *
>
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Received on Tue Feb 13 2018 - 08:00:03 PST
