No default type errors -NH2 and COO- amino acid termini patches for pH 10 simulations – User discussions

GROMACS version:2022
GROMACS modification: No
Much thanks for any help and guidance on these errors – I am studying mixtures of amino acids at pH 10; at this pH the N-term is neutral NH2 and the C-term is negative COO-. I am using the charmm27 force field to parametrize and patch each amino acid. However I’m getting errors that I thought would taken care of with the C and N term nbd files. These are the errors I’m getting along with snippets of my topology files. Thanks again for your time and effort reading this.

ERROR 1 [file phe.top, line 136]:
No default U-B types
——————————-My input to this post————–
Topology file line 136: (1 4 20. 5)
atoms: (1 NH2 2 PHE N)
(4 CT1 2 PHE CA)
(20 CC 2 PHE C)

The NH2 amino acids.n.tdb file is:
[ NH2 ]
[ replace ]
N NH2 14.007 -0.96
CA CT1 12.011 0.19
HA HB 1.008 0.09
[ add ]
2 4 HT N CA C
H 1.008 0.34 -1
[ delete ]
HN

This angle does not seem to be defined in the aminoacids.n.tdb file

  1. Is this a typo for an angle that was not inserted?
  2. Does a parametrization exist for this angle?

————-My input to this post————–

ERROR 2 [file phe.top, line 172]:
** No default Proper Dih. types**

2 1 4 20 9 (line 172)

2 H 2 PHE HT1
1 NH2 2 PHE N
4 CT1 2 PHE CA
20 CC 2 PHE C

From what I think this dihedral seems to be defined in the aminoacid.n.tdb file

  1. What am I missing?

end————-My input to this post————–

ERROR 3 [file phe.top, line 175]:
** No default Proper Dih. types**

start————-My input to this post————–
3 1 4 20 9 (line 175)

3 H 2 PHE HT2
1 NH2 2 PHE N
4 CT1 2 PHE CA
20 CC 2 PHE C

From what I think this dihedral seems to be defined in the aminoacid.n.tdb file

  1. What am I missing?

end————-My input to this post————–


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