[gmx-users] atom types not found

pbuscemi pbuscemi at q.com
Thu Sep 27 18:44:39 CEST 2018 

Alex, 
This pertains the prior correspondence to building a polymer and is the process I've been developing.

To date I can  obtain an ITP and pdb from ATB for a monomer.  From there with information in those files, it is relatively easy to construct the n2t file to use in x2top.  (  I’d be happy to provide an example as a 'tutorial' of sorts).  X2top provides the monomer rtp for use in pdb2gmx. It has all the atom type information.  Thanks for the guidance on that.

The hangups are not associated with the rtp but of all things producing the pdb of the polymer specifically  positioning along,say, the x axis but more importantly, producing the pdb of the polymer that uses the same atom labels as the original pdb of  the monomer.  In the PE example from gromacs there  are 3 mers of 2 atoms  so it is easy to manually keep track of the names, but not if you have 1000 mers.  Avogadro renames the added mers. 

Since gromacs can build proteins, and I can tell gmx that the monomer is a protein  ( it wants to think that it is anyway),  I will try to use the same logic to build the  polymer.  More to come.

Paul



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of paul buscemi
Sent: Monday, September 24, 2018 9:52 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] atom types not found

Thank you for the really rapid reply.  I’ll work on it some more and report the outcome
Paul

> 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.
> 
> 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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