I looked for a third time to be safe... and the original has the messed up coordinates (: ptraj is safe! The mdouts are fine across the board though... tricky error to pin down.
Trevor
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, October 01, 2010 6:15 PM
To: AMBER Mailing List
Subject: Re: [AMBER] sander gb post-processing fail
Hi,
Could you provide some more details so it can be determined if a bug
exists in ptraj or not? When you mean ptraj 'decided to screw with
only 4 frames', does it mean the frames were corrupted, dropped, or
something else? Is it reproducible? What is the size of your system in
atoms and how long are the trajectories you are using? What version of
ptraj are you using, and are all the bugfixes applied? Also, are you
100% certain the original trajectories do not contain any issues?
Sorry for the barrage of questions - I just want to fix any problems
that might be in the code. Thanks!
-Dan
On Fri, Oct 1, 2010 at 3:11 PM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> I just want to follow this up with what happened... for some reason when I combined the TIP3 MD trajectories into one for imin=5 processing, ptraj decided to screw with only 4 frames in the -middle- of one of the trajectories. Ptraj did not report any error when processing and the original trajectories are fine. So, point in hand, if for some reason anyone gets that error message... be sure to check the frame coordinates it failed on.
>
> Trevor
> ________________________________________
> From: Trevor Gokey [tgokey.mail.sfsu.edu]
> Sent: Monday, September 27, 2010 2:25 PM
> To: amber.ambermd.org
> Subject: [AMBER] sander gb post-processing fail
>
> Hello,
>
> I got this line at the bottom (not sure if it's even an error) in my mdout file while using sander.MPI (Amber11) to post process and trajectory.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.7936E+02 1.7701E+02 5.7539E+03 SG 2696
>
> BOND = 693.8115 ANGLE = 1705.4697 DIHED = 2288.0264
> VDWAALS = 2873.7781 EEL = -15679.1151 EGB = -2811.2453
> 1-4 VDW = 738.9313 1-4 EEL = 10289.4658 RESTRAINT = 0.0000
> ESURF = 80.2363
> minimization completed, ENE= 0.17935881E+03 RMS= 0.177014E+03
> minimizing coord set # 56129
> iatenvcnt .gt. iemax in icosasurf
>
> and it just quit with no other warning as far as I can tell. I've ran a previous trajectory successfully with the same input, which I extracted from mmpbsa.py (except the ioutfm=1 part):
>
> 1ANE 115 ns
> &cntrl
> ntb=0, idecomp=0, cut=999.0, nsnb=99999,
> imin=5, maxcyc=0, ncyc=0, igb=5,
> saltcon=0, intdiel=1, extdiel=78.3,
> gbsa=2, surften=0.0072,ioutfm=1
> &end
>
> What should I do seeing an error like that? The only thing I can extrapolate from the error message is that the (i)nternal(e)nergymax in icosasurf(surften issue) has something wrong. Am I far off?
>
> Thanks,
> Trevor Gokey
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Received on Fri Oct 01 2010 - 21:30:05 PDT
