Re: [AMBER] Problem met in running GBn2 model

From: David A Case via AMBER <>
Date: Sun, 22 Jan 2023 12:59:17 -0500

On Sun, Jan 22, 2023, Jiaan Zhu via AMBER wrote:
> I’m trying to run simulations for a 8-mer ssDNA with artificial
> nucleotides by GBn2 model.

In addition to what Carlos said: I'm concerned that your modified DNA
residues (DHY, DFX, DF, DH) are not recognized in the the code as being
"nucleic acid residues", in the isnucat() routine in egb.F90 (in sander).

This would result in getting incorrect neck parameters assigned to the atoms
in those residues. Since things seem to work well withouth modified
nucleotides, it might be that you just need to tell Amber about your
modified residue names. Seems worth a try....look at the egb.F90 code, in
the isnucat() subroutine. Doesn't look that hard to modify.

Of course, the problem could be somewhere else entirely, but this issue
needs to be addressed in any case.


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Received on Sun Jan 22 2023 - 10:00:03 PST
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