Hi Matias,
Thanks for the correction- I had forgotten to attach the unmodded version
of the frcmod, but it turned out the problem wasn't in the frcmod itself,
but an issue with the connectivity in the lib file. Which may be why it was
managing to read and only getting stuck on the write step.
For self-reference and in case anyone else runs into this issue, the issue
was in the connect array- it was reading orginally as
!entry.IC.unit.connect array int
> 1
> 32
> ...
> !entry.IC.unit.residueconnect table int c1x int c2x int c3x int c4x
> int c5x int c6x
> 1 32 0 0 0 0
>
Since I was using the format for an internal nucleotide (eventual end
point) but since at this stage since it's still a nucleoside, it needed to
be in the nucleoside format since it isn't connected to anything yet-
!entry.IC.unit.connect array int
> 0
> 0
> ...
> !entry.IC.unit.residueconnect table int c1x int c2x int c3x int c4x
> int c5x int c6x
> 0 0 0 0 0 0
>
Best,
Kenneth
On Fri, Feb 12, 2021 at 7:14 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Hung,
>
> First, there is no section DIHEDRAL in your frcmod file, that explains the
> message "No torsion terms for CM-N*-CA-NC" and the result "Parameter file
> was not saved". I can't check the dihedral issue without dihedrals and the
> test.off file...
>
> Second, your file frcmod.ic5 seems to be miss-formatted... The section
> "MASS" is required, even if it is empty... that is very important for
> properly parsing the file... then your file should read:
>
> ic5 test
> MASS
>
> BOND
> CA-N* 424.0 1.383 use C -N*
>
> ANGLE
> CM-C -NC 70.0 114.10 use CM-C -NA
> CM-N*-CA 70.0 121.20 use CM-N*-CT
> N*-CA-NC 70.0 123.30 use NA-CA-NC
> N*-CA-N2 70.0 119.30 use N2-CA-NC
> CT-N*-CA 70.0 121.20 use CM-N*-CT
>
> DIHE
> ...
>
>
> Best,
>
> MatÃas
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Kenneth Huang" <kennethneltharion.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Jueves, 11 de Febrero 2021 19:08:58
> Asunto: [AMBER] leap hangs on dihedral in frcmod?
>
> 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 Fri Feb 12 2021 - 14:30:03 PST
