On Sat, Mar 29, 2014 at 7:16 AM, Souvik Sur <souviksur.hotmail.com> wrote:
> Dear Amber user,
> I have a problem regarding running initial steps of my system using AMBER
> 12. I have made input files step by step: minimzation > heating > density
> eq. > equilibration > MD.
> Using the same .prmtop file, I got data up to heating but beyond heating,
> it showed
> error:++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Note:
> 1-4 VDW scale factors are being read from the topology file.Error: Bad
> topology file. Sum of ATOMS_PER_MOLECULE does not equal
> NATOM.+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> I am attaching my all input file as attachment. Please look into it and
> inform me where I was wrong.
>
This is indicative of a tleap bug. You can either use cpptraj or ParmEd
to fix your system. Using ParmEd, it would work like this:
parmed.py << EOF
parm your.prmtop
loadRestrt your.inpcrd
setMolecules
outparm your_fixed.prmtop your_fixed.inpcrd
EOF
Then use the your_fixed.prmtop and your_fixed.inpcrd file.
If you google "Sum of ATOMS_PER_MOLECULE does not equal NATOM", it will
bring you to discussions of this problem. (Such preliminary searches are
always a good idea).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Mar 29 2014 - 10:30:07 PDT
