[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

James Starlight jmsstarlight at gmail.com
Fri Dec 14 21:20:43 CET 2012


in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon for me because in that case the atom names werefrom
standart charmm ff but the total number of errors was bigger than in
case of Swiss params non-standart names usage).

By the way I've simulated choromophore produced by SWISS ( with the
charges assigned from the paper) in the vacuum and didnt notice any
inaccuracy in the conformation of chromophore. So the last that I
should is the carefull assignment of the 9 missed dihedral terms with
the rest of the protein.


2012/12/14, Justin Lemkul <jalemkul at vt.edu>:
> On 12/14/12 2:28 PM, James Starlight wrote:
>> Today I've tried to rename atoms from Swiss's params specific names to
>> the standard charmm names and obtain the set of the same errors
>> No default Improper Dih. types
>> No default U-B types
>>   No default Bond types
>> Its strange to me because chromophore itself consist of only one
>> uncommon bond  (in cyclized ring which could produce only several
>> additional angles and dihedrals)
>> By comparison in the case of Swiss atom names the total amount of the
>> same errors was only 9 (all erors about unknown dihedrals with
>> theadjacent residues. Although I've added capes in that model which
>> mimicks adjacent residues) it's difficult recognize suitable dihedral
>> types.
>> Do you know any others attemps to simulate GFP with chromophore in
>> charmm with proof parameters ?
> This was linked before, at least once:
> http://pubs.acs.org/doi/abs/10.1021/jp014476w
> The authors provide parameters for everything you need.  We used these
> several
> years ago.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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