An enhanced version of SMMP—open-source software package for simulation of proteins

We describe a revised and updated version of the program package SMMP ( Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192–212]. 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. This announcement describes the first major revision of this software package and its newly added features. Title of program:SMMP Catalogue identifier:ADOJ −v2 −0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADOJ_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating system under which the program has been tested:LINUX system Programming language used:FORTRAN Computer:PC Pentium Number of lines in distributed program, including test data, etc.:18 492 Number of bytes in distributed program, including test data, etc.:278 995 Distribution format:ASCII Card punching code:ASCII Catalogue Identifier of previous version:ADOJ Journal Reference of previous version:F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192–212 Does the new version supersede the previous version?:Yes Nature of physical problem:Molecular mechanics computations and Monte Carlo simulation of proteins Reasons for the new version:Increased functionality Summary of revisions:Changes in energy function and protein representation; differences in program structure and organization; new functionalities added; miscellaneous changes and additions Method of solution:Utilizes ECEPP2/3 and FLEX potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles Restrictions on the complexity of the problem:The consumed CPU time increases with the size of protein molecule Typical running time:Depends on the size of the molecule under simulation Unusual features of the program:No