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 - 04:30:04 PST
