n't need to add anything extra for your residue there if it
> doesn't do anything like a disulphide would.
>
> Cheers
>
> Paul
>
>
> On 2018-05-22 09:24, Hemalatha Jayabal wrote:
> > Hi all,
> >
> > I have added a residue (Hydroxyproline) to my .rtp fil
Hi all,
I have added a residue (Hydroxyproline) to my .rtp files and have updated
the hdb and ffbonded files. While browsing through the manual about
specbond.dat, it says that any "special bonds" are to be listed
specifically here. Does this mean for the newly added residue also, the
bond
1.008 ; qtot 1.18
On 11-May-2018 12:06, "Hemalatha Jayabal" <hemalathajaya...@gmail.com>
wrote:
I applied the said terminus as well but I ended up getting the same error.
[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1
; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18
Thank you!
On Fri 11 May, 2018, 00:11 Justin Lemkul, <jalem...@vt.edu> wrote:
>
>
> On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:
> > The magnitude of the charge is 0.18 and I hope such magnitude cannot be
> > ignore
t; On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> > Hi all,
> >
> > I have added a non standard amino acid 'Hydroxyproline' to my forcefield
> > (from literature) Charmm27 and after using pdb2gmx i could see that the
> > system has a non integer charge value for 1 prote
Hi all,
I have added a non standard amino acid 'Hydroxyproline' to my forcefield
(from literature) Charmm27 and after using pdb2gmx i could see that the
system has a non integer charge value for 1 protein chain out of 3 protein
chains. (All 3 chains contain the non standard amino acid)
The
as to whether the dihedral parameters from ffbonded could be
re-ordered for this case and could be used. (The order mentioned in
topology but parameters for same dihedral in ffbonded)
I hope I am clear regarding my query
Regards
Hemalatha Jayabal
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