Hi Dears,
I am trying to generate parameter and topology files for my system using tleap module, but the system includes standard and non-standard residues while these residues have connected to each other.
So I became confused how to do this.
I tested following way:
I discontented the non-standard residue from the system and generated parameter and topoloogy files using antechamber and then prepared following tleap script to combine standard and non-standard residues. (I removed H atoms form connection domains and defined bonds between standard and non-standard residues) But the result is not satisfied. A lot of topology and parameter error is appeared and the generated bonds are not displayed on the systems.
I would be grateful for any advice.
set default PBradii mbondi2
source leaprc.ff99SB
source leaprc.gaff
source leaprc.GLYCAM_06j-1
loadamberprep UNK.prep
loadamberparams UNK.frcmod
m = loadpdb 4GA.pdb
lig = loadpdb UNK-poly.pdb
remove lig.8 lig.8.H11
remove lig.9 lig.9.H11
remove lig.10 lig.10.H11
remove lig.11 lig.11.H11
remove lig.12 lig.12.H11
remove lig.13 lig.13.H11
remove lig.14 lig.14.H11
remove m.1 m.1.H6O
remove m.2 m.2.H6O
remove m.3 m.3.H6O
remove m.4 m.4.H6O
remove m.5 m.5.H6O
remove m.6 m.6.H6O
remove m.7 m.7.H6O
bond lig.8.C1 m.1.O6bond lig.9.C1 m.2.O6
bond lig.10.C1 m.3.O6
bond lig.11.C1 m.4.O6
bond lig.12.C1 m.5.O6
bond lig.13.C1 m.6.O6
bond lig.14.C1 m.7.O6
COM = combine {m lig}
saveamberparm COM test.prm7 test.rst7
solvateBox TIP3PBOX 10.0
saveamberparm COM test.wat.prm7 test.wat.rst7
check m
charge m
quit
Berk.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 20 2015 - 08:30:02 PDT
