Hello everyone,
I am trying to produce the parameters and coordinates files for this pdb (attached here). Please note that the two chains are separated by TER lines: one between the two chains and one at the end. They also have different chain identifiers. When I visualize the pdb in VMD, the two chains are distinguishable (colored differently). However, when I run tleap (code attached below), then visualize the parameters and coordinates files produced from tleap (were too big to attach here but can be reproduced using the attached pdb and tleap files), the chains are indistinguishable. Can someone please let me know if I'm missing something here?
source leaprc.protein.ff19SB
source leaprc.water.opc
x = loadPDB 7uqa_clean.pdb
addions x Na+ 0.0
addions x Cl- 0.0
solvatebox x OPCBOX 12.0
setbox x vdw
savepdb x apo_smurfp.pdb
saveAmberParm x apo_smurfp.parm7 apo_smurfp.rst7
quit
Thanks,
Noureen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 10 2024 - 15:30:02 PDT
