[gmx-users] atom types not found
jalemkul at vt.edu
Tue Sep 25 03:47:42 CEST 2018
On 9/24/18 9:42 PM, paul buscemi wrote:
> 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 ?
x2top requires an .n2t file for any force field.
Sadly, my wiki page on .n2t files was somehow lost, so I will try to
repeat it here, in column numbers:
1. Element (e.g. first character of the atom name)
2. Atom type to be assigned
3. Charge to be assigned
5. Number of bonds the atom forms
6-onward. The element and reference bond length for N bonds (where N is
specified in column 5); x2top will assign a bond if the detected
interatomic distance is within 10% of the reference bond length
> 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 ?
It's not that the atom type isn't found, it's that x2top can't assign an
atom type because a given atom does not satisfy all of the requirements
of the .n2t file listed above. That means a bond tolerance likely isn't
> 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.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users