From amir@genie.terra.co.il Wed Feb 7 05:11:06 1996 Received: from genie.terra.co.il for amir@genie.terra.co.il by www.ccl.net (8.6.10/950822.1) id FAA15026; Wed, 7 Feb 1996 05:09:56 -0500 Received: from merlin.terra.co.il (merlin.terra.co.il [194.90.101.41]) by genie.terra.co.il (8.6.12/8.6.12) with SMTP id KAA14674; Wed, 7 Feb 1996 10:06:38 GMT Date: Wed, 7 Feb 1996 12:08:44 +0200 (IST) From: Amir Gil X-Sender: amir@merlin.terra.co.il To: BBS CHARMM cc: CHEMISTRY@www.ccl.net Subject: trajectory files - summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello netters! Yesterday I sent a question concernning the translation of trajectory files from ALPHA machine to SGI machine. I got plenty of answers and I want to summarize them for you. I will put in only the most usefull ones, to make it short. Thanks to all the reponders, for their time and help. Amir ############################################################################ From: Steve Lionel 06-Feb-1996 0914 -0500 To: amir@genie.terra.co.il Subject: RE: binary files on SGI and ALPHA processors Compile with -convert big_endian. The Alpha is a "little endian" byte order machine, while the SGI is "big endian". This refers to whether the least significant bits are in the lowest addressed byte (little endian) or highest addressed byte (big endian). If you specify -convert big_endian on the command line, DEC Fortran will read and write binary data files using big endian format. You can also select big_endian for specific units - for further information, please see the appendix on "Converting Unformatted Numeric Data" in the DEC Fortran User Manual. Steve ############################################################################ From: Walter Polkosnik To: amir@genie.terra.co.il Cc: chemistry@www.ccl.net Subject: Re: CCL:CHARMm trajectory files-difference between SGI and alpha outputs Different computer architectures store data differently, because of microprocessor hardware details. In order to convert your DEC files to SGI, you first must use the DYNA FORM command on the DEC DCD files to convert the files to text (DHX) format. You then need to ftp those files to the SGI and run the text files through DYNA UNFORM in CHARMm. I have done this before to convert Cray files to SGI files. If you need ore information I can send you my CHARMm input files that do this. ############################################################################ From: "Eldbjoerg S. Heimstad" To: Amir Gil Subject: Re: CCL:CHARMm trajectory files-difference between SGI and alpha outputs Hi, Here is an example script file for converting DCD files to DHX files (formatted) : --------- * Converting binary dcd-files to formatted dhx-files * Remember to convert the dhx-files to dcd files on your * personal machine OPEN READ UNIT 11 FILE NAME "/tmp2/eldbjorg/AMINO.BIN" READ RTF UNIT 11 FILE CLOSE UNIT 11 OPEN READ UNIT 02 FILE NAME "/tmp2/eldbjorg/PARM.BIN" READ PARAMETERS UNIT 02 FILE CLOSE UNIT 02 open read unit 07 card name str_34a.psf read psf card unit 07 close unit 07 OPEN READ UNIT 08 CARD NAME str_34a_min.pdb read coor pdb unit 08 close unit 08 OPEN READ UNIT 50 FILE NAME "str34_300k_260-300.dcd" open write unit 61 card name "str34_300k_260-300.dhx" dyna form first 50 nunit 1 output 61 STOP ------------------------------- And here is an example of converting DHX-files to DCD-files: ------------------------- OPEN READ UNIT 11 FILE NAME $CHM_DATA/AMINO.BIN READ RTF UNIT 11 FILE CLOSE UNIT 11 OPEN READ UNIT 02 FILE NAME $CHM_DATA/PARM.BIN READ PARAMETERS UNIT 02 FILE CLOSE UNIT 02 OPEN READ UNIT 12 CARD NAME $CHM_DATA/MASSES.RTF READ RTF UNIT 12 CARD APPEND CLOSE UNIT 12 OPEN READ UNIT 77 CARD NAME $CHM_DATA/IONS.RTF READ RTF CARD UNIT 77 APPEND CLOSE UNIT 77 open read unit 07 card name str_34a.psf read psf card unit 07 close unit 07 OPEN READ UNIT 08 CARD NAME str_34a_min.pdb read coor pdb unit 08 close unit 08 OPEN READ UNIT 50 CARD NAME str34_300k_140-180.dhx open write unit 61 file name str34_300k_140-180.dcd dyna unform input 50 output 61 STOP ------------------------- Good luck, ####################################################### # Eldbjoerg Sofie Heimstad # # Protein Crystallography Group # # University Of Tromsoe, IMR # # 9037 Tromsoe, NORWAY phone: +47-776-45706 # # +47-776-44737 # # fax : +47-776-44765 # # E-mail: Eldbjorg.Heimstad@chem.uit.no # # URL: http://www.chem.uit.no/KJEMI/heimstad.html # ####################################################### ############################################################################ That's about it Thank you all Amir !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Amir Gil ! ! Chemical and Application engineer ! ! Terra Computers ! ! Ashuah 6 st. ! ! Omer ! ! ISRAEL 84965 ! ! Tel. 07-467502 ! ! Fax. 07-467475 ! ! E-Mail amir@genie.terra.co.il ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!