Re: [AMBER] Tutorial B0

From: Sanmeet Chahal <>
Date: Wed, 4 Mar 2015 16:29:24 -0500

Hello all,

I have been trying to send the following message but I don't think it has
reached you as I do not see it present in the AMBER Mailing list archive,
please excuse me if this has reached you and you hadn't had the time to

I am attaching the prmtop and inpcrd files for all three runs that
succeeded as well as the the case were it failed (the one for acetic acid).

Legend for the prmtop and inpcrd files attached:
prmtop, inpcrd correspond to the same molecule show in Tutorial B0.
prmtop2, inpcrd2 correspond to the molecule shown in Tutorial B0 but the
methyl group removed from the central carbon.
prmtop3, inpcrd3 correspond to the molecule shown in Tutorial B0 with atoms
on half the molecule being removed.
prmtop4, inpcrd4 correspond to acetic acid (that failed).

I have also attached the input files that I used (they were the same for
all the runs) and the 01_Min.out and 01_Min.mdinfo files for the run that

Also I was using sander from Amber14.

I am sending three emails to keep the size of the attachments below the
requirements. In this message you will find all the *.in files, the first
set of prmtop and inpcrd files and the 01_Min.mdout and 01_Min.out files
for the run that failed.


On Wed, Mar 4, 2015 at 8:10 AM, David A Case <>

> On Tue, Mar 03, 2015, Sanmeet Chahal wrote:
> >
> > 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:
> >
> > 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.
> We will need to get the actual prmtop and inpcrd files to try to debug
> a segfault problem. Was there any output in the mdout file from the
> minimzation step that failed?
> ...thanks...dac
> _______________________________________________
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Received on Wed Mar 04 2015 - 13:30:02 PST
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