[AMBER] QM/MM stops at step 2114

From: Corum, Katharine W <katharine-corum.uiowa.edu>
Date: Mon, 15 Aug 2016 15:08:25 +0000

Good morning,


I am trying to run a QM/MM calculation on some proteins using Amber16. I did the NMA tutorial and I based my calculation off of that. After I ran the first protein (output on the left in the image at the bottom) I thought the QM region of the structure was optimized due to the fact that the output says final results. I was excited and moved onto more calculations (middle and right image). However each calculation stops at NSTEP 2114. I don't think this is a coincidence. I think I need to restart the calculation from the rst file but I am not sure how to do that. Is that what I should do since I don't think the QM region is optimized? Below is the input file. I used the same parameters for all 3 calculations but the qmmask value differs for all 3. I also put each protein into a box of water molecules using tleap.


Thank you in advance! - Katie


Initial min of our structure QMMM
&cntrl
 imin=1, maxcyc=5000, ncyc=2000,
 cut=20.0, ntb=1, ntc=2, ntf=2,
 ifqnt=1
/
&qmmm
 qmmask= ':7,70,181,183,511'
 qmcharge= -1,
 qm_theory='PM3',
 qmshake=1,
 qm_ewald=1, qm_pme=1
/



[cid:f63808ed-e6d3-48cc-b268-813ea3db799b]





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Received on Mon Aug 15 2016 - 08:30:04 PDT
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