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<div class="moz-cite-prefix">Hi,<br>
<br>
For point 1, yes I agree circular molecule generation would be
useful. This is not difficult, just a matter of not using termini
and looking up the neighbor residue indices periodically. I have
needed this once and did not have/take the time to implement this
in pdb2gmx. Are you sufficiently good a programming that you could
attempt to add this feature yourself?<br>
<br>
For point 2, is it sufficient to add the name to residuetypes.dat?
Using the concept of a chain sounds nice in principle, but I don't
know if this is used consistently in pdb.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2020-06-10 23:58, Boris Timofeev wrote:<br>
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<div>Dear gromacs developers!</div>
<div>I want to discuss the actual questions.<br>
Do we need to adjust/redefine some the pdb2gmx paradigms?</div>
<div> </div>
<div>1. Unfortunately, pdb2gmx does not know how to work with
ring/circular molecules.<br>
The terminals must be defined as for proteins, and for
dna/rna.</div>
<div>At the same time, interest to circular structures found
quite a lot, growing, and it is quite difficult to make such a
topology manually,<br>
because this operation involves atoms removing , renumbering,
corrections of charges.</div>
<div>Such work will not take much time and effort, but will be
very useful in the future.<br>
Examples of ring structures 5zo6.pdb, 2oiu.pdb, 2kjf.pdb</div>
<div><br>
2. The concept of a "group" of "Protein", "DNA", "RNA", being
conditional, greatly complicates the construction of<br>
complex molecules containing "non-standard" elements in their
chain.</div>
<div>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<br>
described in the external rtp-file, but not included in
residuetypes.dat, into the protein chain,causes an error.<br>
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.</div>
<div>Attempts to modify oligonucleotide terminals also lead to
the need to include the compounds in to the group "DNA"/"RNA"<br>
(depending on the task) , which are not related to them, for
example, fatty acids.<br>
Maybe it makes sense to change the error on a warning about
the heterogeneity of the chain<br>
and include the concept of "CHAIN" into the group?<br>
<br>
It is very interesting to know your opinions and discuss any
interface details.</div>
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<div> </div>
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<div>--<br>
Boris Timofeev</div>
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<br>
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