Sounds like the water residue name is not being mapped to the triangular-bond TIP3 model. What is your water residue name?
Bill
<div>-------- Original message --------</div><div>From: Chitrak Gupta <chgupta.mix.wvu.edu> </div><div>Date:10/02/2015 4:03 PM (GMT-08:00) </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] TIP3 water not recognized </div><div>
</div>Hi,
I am trying to use chamber 14 to generate AMBER inputs. I am using xplor
extended formatted PSF file for this. chamber runs fine, but when I try to
run AMBER (pmemd.cuda version), I am getting the following error:
Hydrogen atom 26802 appears to have multiple bonds to atoms 26801 and 26803
which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
My system has protein, lipid and waters, and the pdb/psf files were
generated by charmm-gui.org
Does anyone know how I could fix this?
Regards,
Chitrak.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 02 2015 - 18:30:03 PDT
