Dear Monia,
this seems a question for GLYCAM mailing list ;) but I try to help, since I have simulated HA as well.
How did you build the protonated glucuronic acid?
I also see an error related to .itp file. According to my statistically - not - meaningful experience, this extension is usually employed with gromacs. Which software do you use?
Best regards,
Tommaso
________________________________________
Da: monia kam [moniakamli95.gmail.com]
Inviato: martedì 19 marzo 2019 16.15
A: amber.ambermd.org
Oggetto: [AMBER] Hyaluronic acid using Glycam06
Hello,
Sorry if my question may seem a bit stupid so i did an MD simulation for
the deprotonated Hyaluronic acid using Glycam06 it worked perfectly, then i
wanted to do the same thing for the protonated version of the acid by
modifying the prep file 9GLYCAM_06h.prep) and adding the sequence 0ZBP but
when applying the energy minimization i get those errors:
ERROR 1 [file HAP.itp, line 104]:
No default Bond types
ERROR 2 [file HAP.itp, line 325]:
No default Angle types
ERROR 3 [file HAP.itp, line 327]:
No default Angle types
ERROR 4 [file HAP.itp, line 450]:
No default Proper Dih. types
ERROR 5 [file HAP.itp, line 452]:
No default Proper Dih. types
ERROR 6 [file HAP.itp, line 454]:
No default Proper Dih. types
ERROR 7 [file HAP.itp, line 464]:
No default Proper Dih. types
ERROR 8 [file HAP.itp, line 465]:
No default Proper Dih. types
So right now i don't know what to do
--
*Monia KAMLY,*
*Ingénieur en Chimie Analytique et Instrumentation,*
*Etudiante Master 2 Chimie, Spécialité, Agro-ressources Biomolécules et
Innovations*
*Faculté des Sciences et Techniques, Université de Limoges.*
*123 Avenue Albert Thomas, 87000 Limoges*
*Mobile: 06 99 78 86 29*
*Email: monia.kamly.etu.unilim.fr <amina.ben-chaaben.etu.unilim.fr>*
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Received on Wed Mar 20 2019 - 04:30:02 PDT
