Oh, I see...
It looks like I'll need to end up writing a short script that does the
loop along the trajectory together with a correct RMS calculation.
Thanks for the tip, Carsten.
Cheers,
Albert
On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote:
> Hi Al,
>
> based on my experience runnin
Dear pymol users
I have one pdb file containing two peptides. Based on experimental data,
I should connect two peptides to obtain one new peptide in pdb file. This
connection is as follows:
CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from
peptide 2.
How to make this connecti
Hi Leila,
Are the peptides already positioned correctly? Then there's nothing you can
do with Pymol to help out with Gromacs. With Gromacs, you'll have to make a
special bond to account for the link between the peptides, and you have to
merge the two peptides during the processing with pdb2gmx. Ch
Hi Leila,
This too is more a question for the Gromacs mailing list.
Gromacs does not read bond information (CONECT records) from a PDB file. It
only reads the ATOM/HETATM records and sets bonds based on the force field
building block definitions and the special bonds (such as the isopeptide
link)
Hello:
I am trying to see the effect of side-chain fluctuation on molecular
permeation through a transmembrane protein channel.
The idea is create a pdb file with a column of B-values related to the RMSF
values of the MD trajectory.
What I tried was to set the B-values of all heavy atom main-ch
Hi Angelo,
As far as I understand the putty representation takes the values from the
b-factor of the Ca atom. Probably you should store your fluctuation values
either on the Ca (leaving all the others atoms with 0.0 or any other value)
or just set the same b-factor for all the atoms of a given res
