[AMBER] Leap ff10 and Sodium ion

From: Johannes Zuegg <j.zuegg.imb.uq.edu.au>
Date: Thu, 24 Oct 2013 10:05:56 +1000

Hi all,


I was trying to build a model using ff10 (tleap> source leaprc.ff10), and
after neutralizing the model (tleap> addions m01 Na+ 0) I tried to save it
(tleap> saveamberparm m01 .) but it complains that it does not have
parameters for Na+


"For atom: .R<Na+ 36000>.A<Na+ 1> Could not find vdW (or other) parameters
for type: Na+"


Looking into parm10.dat I noticed there is no entry for Na+, even though
ions10.lib has some entries for Na+.


Is there a reason for leaving out Na+ from parm10.dat ?


If not, can I just add the corresponding entries from parm99.dat into


I used to run my protein/DNA models with ff99SB (no problem with Na+), but
according to the AmberTools13 document ff10 is recommend ..






Dr Johannes Zuegg

Institute for Molecular Bioscience

The University of Queensland

St Lucia, QLD, 4072


Phone: +61 7 3346 2747

Fax: +61 7 3346 2090

Email: j.zuegg.uq.edu.au

Skype: j.zuegg.uq

www: cddd.imb.uq.edu.au

www: cooper.imb.uq.edu.au


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Received on Wed Oct 23 2013 - 17:30:03 PDT
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