[gmx-users] atom types not found
pbuscemi at q.com
Tue Sep 25 04:52:31 CEST 2018
Thank you for the really rapid reply. I’ll work on it some more and report the outcome
> On 24,Sep 2018, at 9:04 PM, Alex <nedomacho at gmail.com> wrote:
> 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.
> 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.
>>> 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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