On 2/12/18 3:09 PM, farial tavakoli wrote:
First, please note that this line is not doing anything:
define = -DUSE_OLD_C3
If you're trying to use the old CHARMM36 parameters, and not CHARMM36m,
the correct keyword is -DUSE_OLD_C36. We only included that in the case
that people
Hi Justin and Roland,
we are interested in simulating a glycosilated protein. We already have a
pdb file (and psf topology) with the charmm/namd format/nomenclature. We
managed to have pdb2gmx read the carbohydrate residues by adding the
relative entries in the residuetypes.dat, however we have
On 4/10/14, 2:51 AM, gsettanni wrote:
Hi Justin and Roland,
we are interested in simulating a glycosilated protein. We already have a
pdb file (and psf topology) with the charmm/namd format/nomenclature. We
managed to have pdb2gmx read the carbohydrate residues by adding the
relative
Hi All,
To follow up on a few recent issues that we have discovered and/or have been
reported here, we have updated our CHARMM36 force field files. As always, they
can be downloaded from:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
Here is a list of changes:
1. An error in
Dear Justin,
Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn
bound to H2O (water) in updated CHARMM36 ff? For example, this state is
important for some structures. E.g. Carbonic anhydrase.
Ahmet Yıldırım
18 Mar 2014 tarihinde 18:44 saatinde, Justin Lemkul
On 3/18/14, 1:32 PM, Gmail2 wrote:
Dear Justin,
Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn
bound to H2O (water) in updated CHARMM36 ff? For example, this state is
important for some structures. E.g. Carbonic anhydrase.
No. We don't have any special
Nice trick - I didn't realise you could chain and group sed regular
expressions that way!
Neither did I know pdb2gmx had an .arn database.
That's two things I've learned... Can I go home now? :-D
Mark
On Mar 10, 2014 7:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
cat $pdbfile | sed
On 3/9/14, 6:28 AM, jim wrote:
I'm confused about the existence of H5'1 and H5'2 atom names in the RNA
nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36
atom name convention. Particularly, why do atoms H2' and H2'' correspond to
the latter, while H5'1 and H5'2 carry
Thanks for the clarification.
*Bonds involving H5' and H5'' in RNA residues should indeed be changed to
the H5'1 and H5'2 nomenclature.*
Even though H5' and H5'' are connected to the same atom, what would be the
problem to keep these H atom names H5' and H5'' instead of changing them to
H5'1
Thanks, but I'll have to ask you something again. :)
On Sun, Mar 9, 2014 at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/9/14, 7:23 PM, Jim wrote:
Thanks for the clarification.
*Bonds involving H5' and H5'' in RNA residues should indeed be changed
to
the H5'1 and H5'2
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