Re: [gmx-users] Fatal error pdb2gmx

2020-04-26 Thread 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

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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-requ...@gromacs.org.

[gmx-users] Fatal error pdb2gmx

2020-04-26 Thread Paolo Costa 
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.

Please, can somebody figure out what cause such errors?

Thanks a lot.


Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
-- 
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-requ...@gromacs.org.