[AMBER] parameters for type: Cl-

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Sun, 10 May 2015 21:08:20 +0300

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,

*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
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
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