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<div>Dear Justin,</div>
<div> </div>
<div>Thank you for your reply.</div>
<div>I am trying to write an opls unied atom forcefield for Tetrahydrofuran (THF). I thought the common way to write a forcefield</div>
<div>is to consider the atomtypes in the atomtypes.atp and choose those types which are suitable for the problem.</div>
<div>(Considering things like the chemical surroundings as well as the charge to be zero)</div>
<div>If I consider opls_071 for example I found the description "CH2 (SP3) ALKANES" which describes the chemical behaviour for</div>
<div>my problem very well, as I think. </div>
<div>I choosed opls_110 because of the description "United-atom Ether CH2 (-O)" because of the </div>
<div>fact that the CH2 is bonded to an oxygen atom there as well.</div>
<div> </div>
<div>So do I just have to choose other atomtypes to build the united atom THF forcefield?</div>
<div>What points do I have to take into account when choosing suitable atomtypes?</div>
<div> </div>
<div>Nevertheless I am wondering, that there are in general no bonding, angle or dihedral parameters for C2 given in the ffbonded.itp. </div>
<div>(For example C2 and C3 or C2 with any arbitrary other atomtype)</div>
<div>Does this mean that the type C2 is never bonded to any other atomtype?</div>
<div> </div>
<div>Best wishes,</div>
<div>Mary</div>
<div> </div>
<div> </div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 30. April 2015 um 14:48 Uhr<br/>
<b>Von:</b> "Justin Lemkul" <jalemkul@vt.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] OPLS force field issue</div>
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<br/>
On 4/30/15 4:46 AM, Mary wrote:<br/>
> Dear gmx users,<br/>
><br/>
> I also try to use the OPLS force field for my simulations. After defining<br/>
> suitable atomtypes:<br/>
><br/>
> opls_110 (type C2)<br/>
> opls_071 (type C2)<br/>
><br/>
> I would like to add the suitable bondtypes, angletypes and so on. But where<br/>
> do I get those parameters for the angles and k?<br/>
><br/>
<br/>
If they're not in the force field, you have to derive them.<br/>
<br/>
> I thought, that the values have to be in the ffbonded.itp.<br/>
><br/>
<br/>
Not necessarily. What leads you to believe that these particular atom types<br/>
should be bonded? You can't necessarily just combine any two types. If the<br/>
parameters are missing, that probably means the types are not what you want for<br/>
whatever it is you're trying to do.<br/>
<br/>
-Justin<br/>
<br/>
> If I am interested in opls_182 for example, which has the bond type CT (I<br/>
> got this information from the atomtypes.atp) I found several informations<br/>
> about CT in the ffbonded:<br/>
><br/>
> [ bondtypes ]<br/>
> ; i j func b0 kb<br/>
> CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file<br/>
><br/>
> [ angletypes ]<br/>
> ; i j k func th0 cth<br/>
> CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file<br/>
><br/>
> But there are no parameters listet for C2.<br/>
> I know that I could also "ignore" the parameters and include the oplsaa.ff<br/>
> in my topology file but is there also a way to get those parameters directly?<br/>
><br/>
> I suppose there is a way, as I found various posts including this<br/>
> parameters as for example in this post.<br/>
><br/>
> (".....> C2 C3 1 0.16020 292880.0 ;..... )"<br/>
><br/>
> Many thanks in advance!<br/>
><br/>
> Mary<br/>
><br/>
><br/>
><br/>
<br/>
--<br/>
==================================================<br/>
<br/>
Justin A. Lemkul, Ph.D.<br/>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br/>
<br/>
Department of Pharmaceutical Sciences<br/>
School of Pharmacy<br/>
Health Sciences Facility II, Room 629<br/>
University of Maryland, Baltimore<br/>
20 Penn St.<br/>
Baltimore, MD 21201<br/>
<br/>
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
<a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br/>
<br/>
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