Re: [AMBER] Tutorial B0

From: Jason Swails <>
Date: Wed, 4 Mar 2015 07:58:59 -0500

> On Mar 3, 2015, at 6:05 PM, Sanmeet Chahal <> wrote:
> Hello all,
> I am a new Amber user and so I followed and completed Tutorial B0 up to the
> point of VMD visualization of the result.
> I am now trying to repeat the tutorial up to this point with a prmtop and
> inpcrd files that I produce using tleap and a customized frcmod file. Here
> are the steps I take:
> 1) Read the .mol2 file that I have produced outside amber and produce a
> corresponding frcmod file for it
> The following are done in tleap:
> 2) source leaprc.ff12SB
> 3) mol = loadMol2 foo.MOL2
> 4) loadAmberParams
> 4.5) check mol (no errors are detected)
> 5) solvateBox mol TIP3PBOX 10.0
> 6) saveAmberParm mol prmtop inpcrd
> Then I try to run through tutorial B0 using these newly produced prmtop and
> inpcrd and the exact same,, files and
> commands given in Tutorial B0:(
> However this fails after the Run Minimization command and gives the
> following error: Segmentation fault (core dumped). First I tried this with
> a .MOL2 file for acetic acid, guanidinium etc. Eventually I created a .MOL2
> file for the same molecule used in the tutorial and produced the prmtop and
> inpcrd files using the same steps 1-6 as above.
> This time with I was able to complete the tutorial. I then tried to modify
> the molecule by removing the methyl on the central carbon and completed
> steps 1-6 and ran through the tutorial again with no trouble. I then
> removed the atoms on one side of the molecule, completed steps 1-6 and ran
> through the tutorial again with no problem. By now the structure was
> extremely close to acetic acid so I modified it again to be acetic acid but
> this time the error again appeared at the Run minimization step of the
> tutorial.
> What is causing the tutorial to fail when I use a prmtop and inpcrd file
> produced from a .MOL2 file for a molecule of certain size but causing it to
> fail for others? And how would I fix it? The problem is particularly
> puzzling since neither the *.in files or commands in Tutorial B0 seem to
> make any reference to molecule size or shape.
> I have attached images of the molecules with which I was able to complete
> the tutorial using prmtop and inpcrd files produced with steps 1-6.
> Thank-you for your help.

This is strange. Segmentation faults are among the most uninformative errors that can occur. Can you send me, off-list, your topology file, coordinate file, and input file that you used? Also tell me whether you used sander, pmemd, or pmemd.cuda for the calculation.

I will try to reproduce this problem.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 05:00:04 PST
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