[gmx-users] atom types not found

[Alex]

I use x2top a whole lot, so here's an example to be considered in the
context of what Justin just wrote:

CJ   opls_xxx    0.0    12.011  3    CJ  0.142   CJ  0.142   CJ  0.142

The total number of bonds is 3, then just list them in pairs of
element-bond entries. If I want a different type assigned to an atom that
only has two nearest neighbors, it'd look like:

CJ   opls_yyy    0.0    12.011  2    CJ  0.142   CJ  0.142

and so on. A very useful utility for doing solid-state stuff with gmx. Hope
this helps.

Alex



The

On Mon, Sep 24, 2018 at 7:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
> -Justin
>
> > 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.
> > UMN
> >
> >
> >
> >
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
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>
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