[gmx-users] Fatal error pdb2gmx

[Justin Lemkul]

On 4/26/20 5:15 AM, Paolo Costa wrote:
> Dear Gromax users,
>
> I created a new residue of 118 atoms within Amber99 force field. However
> when I run the "pdb2gmx" I got many times the following warning: "*WARNING:
> Duplicate line found in or between hackblock and rtp entries" *and in the
> end I got the following fatal error: "*Atom O10 in residue POM 0 was not
> found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea
> what the warning means, however I do not understand the fatal error since I
> am sure that the Atom O1 is present in the residue I created. In attachment
> you can find the .pdb and the .rtp files I created.

The mailing list does not accept attachments. If you want to share 
files, upload them to a file-sharing service and provide a link. Note 
that the error mentions O10, not O1.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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