SMMP v. 3.0 - Simulating proteins and protein interactions in Python']Python and Fortran

被引：20

作者：

Meinke, Jan H. ^{[1
]}

Mohanty, Sandipan ^{[1
]}

Eisenmenger, Frank ^{[2
]}

Hansmann, Ulrich H. E. ^{[1
,3
]}

机构：

[1] Forschungszentrum Julich, John von Neumann Inst Comp, D-52425 Julich, Germany

[2] Leibniz Inst Mol Pharmacol, D-13125 Berlin, Germany

[3] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA

来源：

COMPUTER PHYSICS COMMUNICATIONS | 2008年 / 178卷 / 06期

基金：

美国国家科学基金会;

关键词：

FORTRAN package; protein folding; Monte Carlo; minimization; generalized-ensemble simulations; !text type='Python']Python[!/text;

D O I：

10.1016/j.cpc.2007.11.004

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more. Program summary Title of program: SMMP Catalogue identifier: ADOJ_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADOLv3-0.html Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language used: FORTRAN, Python No. of lines in distributed program, including test data, etc.: 52 105 No. of bytes in distributed program, including test data, etc.: 599 150 Distribution format: tar.gz Computer: Platform independent Operating system: OS independent RAM: 2 Mbytes Classification: 3 Does the new version supersede the previous version?: Yes Nature of problem: Molecular mechanics computations and Monte Carlo simulation of proteins. Solution method: Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles. Reasons for new version: API changes and increased functionality. Summary of revisions: Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings. Restrictions: The consumed CPU time increases with the size of protein molecule. Running time: Depends on the size of the simulated molecule. (C) 2007 Elsevier B.V. All rights reserved.

引用

页码：459 / 470

页数：12