[AMBER] standard and non-standard residues

From: Ramin Ekhteiari <ramin_ekh.yahoo.com>
Date: Sat, 20 Jun 2015 15:09:43 +0000 (UTC)

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

AMBER mailing list
Received on Sat Jun 20 2015 - 08:30:02 PDT
Custom Search