version 5.0.5 : Generation of force vectors corrected to provide uniform random sampling on the surface of a sphere, e.g. as described in :
This correction results in different RAMD trajectories but tests have so far not shown any significant difference in results for a set of RAMD simulations or use of the tauRAMD procedure to compute relative residence times. The biggest effect might be expected in cases with a dependence on the z-axis, e.g. for a binding pocket in a protein channel along the z-axis.
t-random acceleration molecular dynamics (tRAMD) is a protocol for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism.
The approach is based on the RAMD method in which, during a standard molecular dynamics simulation of the bound complex, a small additional randomly oriented force is applied to the compound to facilitate its unbinding. Note, that in the previous RAMD versions acceleration (instead of the force) was used as an input parameter.
tRAMD protocol includes:
(i) system minimization and equilibration
(ii) generation of a set of starting replicas using standard MD simulations with NAMD software
(iii) simulations of RAMD trajectories starting from different replicas
(iv) statistical analysis of the RAMD dissociation times using an R script, which yields relative residence times of compounds
The RAMD license prohibits commercial use of the code. For testing and using RAMD on a commercial basis you need to negotiate a commercial license by contacting us.
HITS gGmbH, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
– hereinafter referred to as “Licensor” or “HITS gGmbH”-
and person accepting the license agreement on the web page
– hereinafter referred to as “Licensee”-
HITS gGmbH represents both HITS gGmbH and the European Molecular Biology Laboratory,
Meyerhofstrasse 1, 69117 Heidelberg, Germany in this agreement as both parties have
developed parts of the software.
The subject matter of this Agreement is the Software
i.e., the latest version available and released for distribution prior to execution of this
Agreement (hereinafter referred to as the “Software”).
Upon request, Licensor shall supply Licensee with free updates of the major version of the
Software acquired by Licensee. The major version is specified by the first digit in the version
number. The provisions governing the Software shall apply to updates accordingly. The
Licensor is under no obligation to make and release updates.
S. K. Lüdemann, V. Lounnas, R. C. Wade “How Do Substrates Enter and Products Exit the Buried Active Site of Cytochrome P450cam? 2. Steered Molecular Dynamics and Adiabatic Mapping of Substrate Pathways” J. Mol. Biol. 2000, 303 (5), 813–830
D. B. Kokh, M. Amaral, J. Bomke, U. Grädler, D. Musil, H.-P. Buchstaller, M. K. Dreyer, M. Frech, M. Lowinski, F. Vallee, M. Bianciotto, A. Rak, R. C. Wade “Estimation of drug-target residence times by t-random acceleration molecular dynamics simulations” submitted to JCTC
If Licensee is a business person, it shall promptly inspect the Software after receipt in
accordance with § 377 German Trade Code and notify Licensor of any defects that are
apparent during the inspection immediately after delivery, and of any hidden defects
immediately after their discovery. Notice of defect shall be given in writing. Licensee shall
describe the defect(s) in writing and as specifically as possible, to the extent that it may be
reasonably expected to do so.
This agreement is effective until terminated. In case a new version of this license agreement
is published, you will be notified 4 weeks in advance. This agreement will terminate
immediately without notice from HITS gGmbH if you fail to comply with any of the terms and
conditions of this license. This agreement will also terminate immediately without notice from
the HITS gGmbH if it is found to implement patented algorithms or contain copyrighted code
not owned or licensed by HITS for the purpose of its inclusion in the RAMD software. This
agreement cannot be terminated by any other mechanism or for any other reason than those
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