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

[Schirra, Simone]

Yes, there is no protein/DNA/RNA in my system. Do I have to define this somewhere? I get the warning when executing pdb2gmx.

-----Ursprüngliche Nachricht-----
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> Im Auftrag von Alessandra Villa
Gesendet: Mittwoch, 4. März 2020 17:26
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] PEG from ATB: No residues in chain

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
>
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