[gmx-users] atom types not found
pbuscemi at q.com
Tue Sep 25 03:42:24 CEST 2018
This is a version of a very old question
Using Avogadro, I’ve built an all atom version of nylon12, ( 45 atoms ) converted to a gro file with editconf. I want to generate the rtp so I can construct a polymer. Using x2top, I’ve tried using both gromos 54a7 ff and oplsaaff. there are two outcomes:
1) if trying 54a7, I am warned that the atomnames2types.n2t is not found ( and indeed it is not present in the ff subfolder ) . I’ve done what I think is an extensive search ( eg github, etc ), but have not found a n2t for 54a7. I tried to construct one following that found in oplsaa but that has not worked out -yet. Does 54a7ff require an n2t file and if so what is the format ?
2) In trying oplsaa, I am warned only 44 of 45 atom types are found.. It turns out that it is the Nitrogen that is the culprit. If I convert the nitrogen to carbon in the gro , file the top and rtp are completed. It’s hard to believe that an amide nitrogen is not in the force field. Thinking it may be my model, I downloaded arginine from “aminoacidsguide.com” to avoid Avogadro. With Aginine only 19 of 26 atoms were found in the oplassff. What ? I can’t make an rtp for arginine without modifying the ffbonded or n2t for oplsaa. Is x2top simply not the right tool ?
Note if I submit the nylon pdb to ATB get back a usable itp, and it is possible to generate a small polymer this way, ( 20 mers or so ). But I should be able to construct a polymer similar to the example given for PE some 9 years ago using a beginning, middle mers. But I need the rtp.
Thanks for any responses
Paul Buscemi, Ph.D.
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