Dear Amber users !
I am preparing system of water soluble protein using tleap with the
following script :
source leaprc.protein.ff19SB
source leaprc.water.opc
prot = loadpdb input.pdb
addIons prot Cl- 0
addIons prot Na+ 0
setbox prot centers
solvateoct prot TIP3PBOX 20.0
savepdb output.pdb
saveamberparm output.prmtop output.prmcrd
quit
Briefly, everything works OK but in the output.pdb I see that the N
and C terminus of the proteins are connected by the artificial
covalent bond despite the large physical distance between them... I
performed a short MD simulation for the system and extracted snapshots
after it and in pymol I see the same thing.
Should the C and N parts be capped to prevent this bug ? If yes, could
you please suggest the modification of my tleap script in order that
the first and the last residues would be automatically capped without
explicit definition of the amino acid ?
Many thanks in advance
Cheers
Enrico
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 05 2023 - 03:00:02 PDT
