Dear Sir
I am trying to prepare force field parameter of *PLP* (pyridoxal 5
phosphate) and i have followed the tutorial
http://ambermd.org/
tutorials/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 *
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 12 2018 - 06:00:04 PST
