Dear Amber list members,
I have on ubuntu linux amber14 and amber tools 15 installed.
Preparing protein by xleap I have faced the error message
(see details below).
What is a correct xleap command for accounting Cl-
counter ions that will avoid the error?
Thank you,
Michael
*xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB*
*>set default PBRadii mbondi2*
*>p1 = loadpdb hp.pdb*
*>addions p1 Cl- 0*
*>solvateoct p1 TIP3PBOX 15*
*>saveamberparm p1 hp.prmtop hp.inpcrd*
*Checking Unit.*
*Building topology.*
*Building atom parameters.*
*For atom: .R<Cl- 153>.A<Cl- 1> Could not find vdW (or other) parameters
for type: Cl-*
*Parameter file was not saved.*
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Sun May 10 2015 - 11:30:02 PDT
