Hi all,
I'm having an odd issue where leap seems to be hanging when I try to write
my prmtop/inpcrd after loading in my frcmod- ie, when I run
source $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff94
> loadamberparams frcmod.ic5
> loadoff test.off
> m1 = loadpdb ic5.pdb
> saveamberparm m1 test.prmtop test.inpcrd
>
> saveamberparm m1 ic5.prmtop ic5.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 6 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
>
It'll hang there without writing anything. I figured it seems to be tied to
the dihedral/improper portion in my frcmod (attached) since when I remove
those sections, it starts complaining
> saveamberparm m1 ic5.prmtop ic5.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> ** No torsion terms for CM-N*-CA-NC
> ** No torsion terms for CM-N*-CA-N2
> ** No torsion terms for CT-N*-CA-NC
> ** No torsion terms for CT-N*-CA-N2
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for N*-NC-CA-N2
> atoms are: N1 N3 C2 N4
> ** Warning: No sp2 improper torsion term for CT-CM-N*-CA
> atoms are: C1' C6 N1 C2
> total 4 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
>
So as far as I can tell, it is reading the frcmod correctly- but is stuck
on the writing part in some way linked to the dihedrals?
Best,
Kenneth
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Thu Feb 11 2021 - 14:30:02 PST
