[gmx-developers] (no subject)

Boris Timofeev boristim at mail.ru
Wed Jun 10 23:58:53 CEST 2020

Dear gromacs developers!
I want to discuss the actual questions.
Do we need to adjust/redefine some the pdb2gmx paradigms?
1. Unfortunately, pdb2gmx does not know how to work with ring/circular molecules.
The terminals must be  defined  as for proteins, and for dna/rna.
At the same time, interest to circular structures found quite a lot, growing, and it is quite difficult to make such a topology manually,
because this operation involves atoms removing , renumbering, corrections of charges.
Such work will not take much time and effort, but will be very useful in the future.
Examples of ring structures 5zo6.pdb, 2oiu.pdb, 2kjf.pdb

2. The concept of a "group" of "Protein", "DNA", "RNA", being conditional, greatly complicates the construction of
complex molecules containing "non-standard" elements in their chain.
On the one hand, a variety of terminal molecules, such as acetic acid, NH2, etc. are included in the group of "Protein" (proteins are in no way), on the other hand, an attempt to include even a protein molecule
described in the external rtp-file, but not included in residuetypes.dat,  into the protein chain,causes an error.
The modification in the DNA sequence of one nucleotide into the RNA, also causes the error, although oligonucleotide chains of heterogeneous elements are now widely used.
Attempts to modify oligonucleotide terminals also lead to the need to include the compounds in to the group "DNA"/"RNA"
(depending on the task) , which are not related to them, for example, fatty acids.
Maybe it makes sense to change the error on a warning about the heterogeneity of the chain
and include the concept of "CHAIN" into the group?
It is very interesting to know your opinions and discuss any interface details.
Boris Timofeev
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