[gmx-users] atom types not found

Justin Lemkul 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
4. Mass
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 
specified here.

> 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 
being satisfied.


> 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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