From chemistry-request;at;server.ccl.net Wed Jul 17 07:08:16 2002 Received: from hermes.csd.unb.ca (root ( ( at ) ) [131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HB8Gv19884 for ; Wed, 17 Jul 2002 07:08:16 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6HB8GqX028452 for ; Wed, 17 Jul 2002 08:08:16 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Wed Jul 17 08:08:15 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA26932 for ; Wed, 17 Jul 2002 08:08:15 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Wed, 17 Jul 2002 08:08:15 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Answers to Number of Atom Types in Autodock Message-ID: <3D3526F1 (+ at +) webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" X-Mailer: WebMail (Hydra) SMTP v3.61.08 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6HB8Gv19885 Thank you to everyone who responded to my question. I have managed to recompile Autodock and Autogrid under Linux using the autocomm.h-extra-maps to replace the original autocomm.h in both Autodock and Autogrid. So now I should have up to 15 atom types available for docking calculations. Note: I tried compiling on my SGI, but the GNU GCC compiler on SGI didn't really like the "make" file, therefore I switched to Linux, which compiled with minimal problems. Below is my original question and the responses. Thanks again to everyone, Robert Original Question: Fellow CCLers, A question on Autodock and the number of atom types allowed in the ligand used for docking. My ligand contains Carbon, Aromatics, Nitrogen, Oxygen, Sulphur, Hydrogens, and Fluorine atoms. Apparently Autodock allows only 7 atom types. When I try to run the docking with this particular ligand, I get the following error message: autodock3: ERROR: ERROR: 7 atom types declared in "", S_line "CANOSHF"; maximum allowed is 6. Change "ATOM_MAPS" in "autocomm.h" autodock3: Aborting... autodock3: Unsuccessful Completion. I found two "autocomm.h" files, and also another called autocomm.h-extra-maps, however changing the contents of the autocomm.h files did not correct the problem. My questions are: 1- Can autodock support more than 6 different atom types per ligand 2- Am I going to have to recompile Autodock in order to be able to use ligands with more than 6 atom types. I will post the answers to the board. Thank you in advance. Robert REPLIES: Hi Rob, did you recompile the code...? i have autodock with up to 15 atomtypes. if you need help to compile or modify the code please email me and i will send you a patch file. you need to modify both autodock and autogrid. its best to hack the files in the src/autodock/autocomm.h and the same for autogrid respectively i did the following #define MAX_MAPS 16 /* Maximum number of energy maps */ #define ATOM_MAPS 14 /* Number of atomic affinity grids */ #define NATOMTYPES 15 /* Number of atom types for atomic interactions */ #define MAX_TYPES 8 /* Maximum number of atom types used. */ then do a make and a make install cheers Kim ************************************************************ I solved this problem by re-compiling autodock. The change required is in the file autocomm.h: change line: #define ATOM_MAPS 6 to be: #define ATOM_MAPS 8 (or however many you need) It sounds like you made this change to autocomm.h already. What is then required is to re-compile the program by typing the command "make". Susan Heffron P.S. In my particular case, on an SGI, I had to make the following changes to the Makefile to get it to run without error messages: old line: OLIMIT = $(CSTD) $(OPT) # SGI, Sun, HP, Convex, >... new line: OLIMIT = $(CSTD) $(OPT) -OPT:Olimit=2442 # Some SGIs. old line: DBUG = -DNDEBUG # No debugging and no assert code. new line: DBUG = # Use assert code. ========================================================================== Thanks, Susan Heffron **************************************** Hi Rob, I have had the same problem. Infact, htis problem has been discussed about two weeks ago in CCL. To answer your questions: 1.No 2.Yes, but you d have to change a great deal of source code, which was, at least for me, beyond my capabilities of programming. I talked to the guys of SCRIPPS and they said it would take some efford to allow more than six atom types, infact they know about this problem. I couldn t figure out why they didnt allow lets say ten types right away. Apart from that, AutoDock works really well. Hope this helps. Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering University of Washington Seattle, WA 98195 email detering ( ( at ) ) u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ I solved this problem by re-compiling autodock. The change required is in the file autocomm.h: change line: #define ATOM_MAPS 6 to be: #define ATOM_MAPS 8 (or however many you need) It sounds like you made this change to autocomm.h already. What is then required is to re-compile the program by typing the command "make". Susan Heffron P.S. In my particular case, on an SGI, I had to make the following changes to the Makefile to get it to run without error messages: change: OLIMIT = $(CSTD) $(OPT) # SGI, Sun, HP, Convex, ... to be: OLIMIT = $(CSTD) $(OPT) -OPT:Olimit=2442 # Some SGIs. change: DBUG = -DNDEBUG # No debugging and no assert code. to be: DBUG = # Use assert code. -- ------------------------------------------------------------------ Susan Heffron Dept. of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 U.S.A. phone: (949) 824-4625 FAX: (949) 824-8540 ------------------------------------------------------------------ In general, a program must be recompiled whenever changes are made to any of the *.h files; these are part of the source code. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable - at - nih.gov ALT email: rvenable -AatT- speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6[ AT ]unb.ca ********************************