[gmx-developers] (no subject)

Berk Hess hess at kth.se
Thu Jun 11 13:14:18 CEST 2020


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?

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.



On 2020-06-10 23:58, Boris Timofeev wrote:
> 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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