Hi,
I recommend upgrading to AmberTools 18. Amber 14 is several years old
at this point and many errors have been fixed since then.
-Dan
On Tue, Dec 11, 2018 at 3:49 AM jacob wick <jacobwick.la.gmail.com> wrote:
>
> Dear all,
>
> I am using the following input file and generated the dry top for complex
> protein and drug using both methods: 1) pdb file (tleap) and 2) trajectory
> (ante-MMPBSA.py)
>
> Still the error in LOG file shows:
>
> CalcError: /opt/apps/amber14/bin/cpptraj failed with prmtop drydock.top!
>
> and the last file generated is _MMPBSA_complex_gb.mdout.0 with last line as:
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> FATAL: NATOM mismatch in coord and topology files
>
>
>
> whereas the number of atoms and format of top and crd both are correct.
> No. of atoms in Complex Dry: 3506
> No. of atoms in Protein: 3427
> No. of atoms in Ligand: 79
> With box complex: 90751 atoms
>
> Also, I am able to generate pdbs from the individual frames and able to
> visualize the trajectory using the box top file correctly. I am also able
> to generate pdb using the drydock.top and drydock.crd via ambpdb. All the
> files show complete pdb without any error.
>
>
> Input file for running GB
> &general
> startframe=1, interval= 25, endframe=1000, strip_mask=":WAT"
> /
> &gb
> igb=2, saltcon=0.0
> /
> &decomp
> idecomp=1, print_res="44; 144-149; 168-172"
> dec_verbose=1,
> /
>
> Pl. guide what could be the possible reason for the error.
>
> Thanks and Regards,
> Jac
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Received on Wed Dec 12 2018 - 09:00:02 PST
