Dear all,
I am trying to compute the free energy of hydration for cellobiose (a
beta (1-4) glucose dimer) using BAR in Gromacs 4.6.1. However, I
encounter a problem.
I find that the vacuum conformations of the molecule in a regular vacuum
simulation differ from the conformations in the decou
On 08/05/2013 01:54 PM, Justin Lemkul wrote:
On 8/5/13 7:44 AM, Joerg Sauter wrote:
Dear all,
I am trying to compute the free energy of hydration for cellobiose (a
beta (1-4)
glucose dimer) using BAR in Gromacs 4.6.1. However, I encounter a
problem.
I find that the vacuum conformations
On 08/05/2013 02:15 PM, Justin Lemkul wrote:
On 8/5/13 8:12 AM, Joerg Sauter wrote:
On 08/05/2013 01:54 PM, Justin Lemkul wrote:
On 8/5/13 7:44 AM, Joerg Sauter wrote:
Dear all,
I am trying to compute the free energy of hydration for cellobiose
(a beta (1-4)
glucose dimer) using BAR in
Hi,
I am building a tetramer of beta(1-4) linked glucose with pdb2gmx
(Gromacs 4.6.3). I have three residue types BGLB BGLM BGLE defined in
the aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.
Using pdb2gmx works fine, until I link the residues via the specbond.dat
fi
es manually by using pdb2gmx -rtpres.
Where would have been a good place for you to have read "Using
three-letter .rtp residue names might make life easier. Consider using
pdb2gmx -rtpres if you need longer names."
Mark
On Thu, Aug 15, 2013 at 3:45 PM, Joerg Sauter wrote:
Hi,
I am b
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