Hi Mark,
Thanks again. Your suggestion of introducing the lauroic acid as a
pseudo-amino acid seems to solve my problem. Below is my corrected
aminoacids.rtp file for the 6-Carbon case as a test. (I used the Berger
lipid parameters.) Just to be sure, could you have a look at the file (I
used
On 4/19/2011 6:55 AM, Emine Deniz Tekin wrote:
Hi Mark,
Thanks again. Your suggestion of introducing the lauroic acid as a
pseudo-amino acid seems to solve my problem. Below is my corrected
aminoacids.rtp file for the 6-Carbon case as a test. (I used the
Berger lipid parameters.)
Looks
Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what you
meant “you can make one that uses backbone-style linking. Most of the
forcefields will have examples of non-amino-acid terminating residues -
these make a single peptide bond just like yours does.”. So, let me
On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what
you meant “you can make one that uses backbone-style linking. Most of
the forcefields will have examples of non-amino-acid terminating
residues - these make a
On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
Hi Gromacs users,
I want to covalently link the lauroic acid to the Valine residue (it
is a peptide (amide) bond), I know that I should update the
specbond.dat.But before updating this file, I need the NH as an N
terminal of the first residue
Hi Gromacs users,
I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat. But
before updating this file, I need the NH as an N terminal of the first
residue (Valine). When I used pdb2gmx with the –ter flag,
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