[gmx-users] PEG from ATB: No residues in chain

[Alessandra Villa]

Hi,

On Wed, Mar 4, 2020 at 4:11 PM Schirra, Simone <Simone.Schirra at uibk.ac.at>
wrote:

> Dear Gromacs users,
>
> I'm totally new to GROMACS and I want to simulate a PEG chain in different
> environment. I found various PEG topologies on the ATB website and tried to
> use them combined with the force field provided on the website. However, I
> always get a warning like this:
>
> "Warning: No residues in chain starting at YAHE identified as
> Protein/RNA/DNA.
> This makes it impossible to link them into a molecule, which could either
> be
> correct or a catastrophic error. Please check your structure, and add all
> necessary residue names to residuetypes.dat if this was not correct."
>
>
The warning says that you have no Protein/RNA/DNA residues and indeed PEG
is polyethylene glycol.
Or do you have also protein/DNA/RNA in the system? Is YAHE  the molname
given to PEG in the topology file? Where do you get the warning?

Best regards
Alessandra

I have tried different topologies, the residues are always named
> differently but they are never defined, although I use the force field that
> ATB specifies for this.
> Also in other databases I could only find PEG with other residues, but not
> somewhere defined. Since it is a well known polymer, I guess that it's well
> defined somewhere and I just need to know the correct name for a r2b file
> or something like that...
> I would be very grateful if someone could help me with this!
>
> Simone
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>