Dear Justin,
1) I can understand the improper for stereocenters (chiral) easily but with
bonds I am confused (I have tried to explain below please let me know if I
have defined impropers correctly for peptide to keep it planar).
H1 O H3
\ I /
--C1---C--N---C2--
/ I \
H2 H H4
So I think improper (being zero) to keep peptide planar should be defined
(and sufficiently) as: O C N C1
and dihedral should be which is simple as: O C N H
But it confuses me, why one needs to define improper for peptide. If I just
keep dihedral angle strict (high force constant) then it will make peptide
freezed! so it will remain planar.
2) Also, I am not sure whether OPLS needs this peptide bond to be defined
with improper, someone have experienced this please suggest?
regards,
On Wed, Jul 17, 2013 at 5:48 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 7/17/13 10:37 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I have some polymer having peptide bond and want to use OPLSaa. I was
>> following Justin's example for building polymers
>> http://lists.gromacs.org/**pipermail/gmx-users/2009-**March/040125.html<http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html>
>>
>> I have few queries:
>>
>> 1) do I need to define improper for peptide in .rtp file to keep it
>> planar?
>>
>>
> If the parent force field uses these terms, yes.
>
>
> 2) Also can pdb2gmx write improper by itself (in out .top file) depending
>> upon bond information and atom types defined in rtp file? Then there will
>> be no need to define impropers in rtp
>>
>>
> There's an easy way to find out :) Otherwise, if you know what you want,
> specify it and be 100% certain.
>
>
> 3) Also can I use + before atom name more than once in one residue
>> (fragmented polymer)
>>
>>
> My gut says yes, but a real example would be helpful. You can certainly
> use the + indicator on multiple lines and (I think) even within the same
> line.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> |
> (410)
> 706-7441
>
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