From tom at compbio.dundee.ac.uk Fri Jan 18 18:03:18 2008 From: tom at compbio.dundee.ac.uk (Tom Walsh) Date: Fri Jan 18 18:03:33 2008 Subject: [Discuss] Re: registration for the tool STAMP (fwd) In-Reply-To: References: Message-ID: <4790E9E6.9030200@compbio.dundee.ac.uk> Hi, I think your problem is owing to the size of 1nfi; it has 1252 residues in it whereas the default value of the MAX_SEQ_LEN parameter is 1000. You can increase this using STAMP's -max_seq_len option. Tom > I am getting an error, while using stamp. > > melaimanik@ieim-57474:~/work/input_files/stamp $ stamp -f > 1nfi_1bi7.cmd -s -n 2 -prefix 1nfi_1bi7 > > STAMP Structural Alignment of Multiple Proteins > by Robert B. Russell & Geoffrey J. Barton > Please cite PROTEINS, v14, 309-323, 1992 > > error: number of coordinates read surpasses memory limit [igetca] > Error in domain 1 object 1 > melaimanik@ieim-57474:~/work/input_files/stamp $ more 1nfi_1bi7.cmd > /home/melaimanik/pdb_files/1NFI.pdb 1 { ALL } > /home/melaimanik/pdb_files/1BI7.pdb A { CHAIN B } > > It works if my input is > /home/melaimanik/pdb_files/1NFI.pdb 1 { CHAIN E } > /home/melaimanik/pdb_files/1BI7.pdb A { CHAIN B } From tom at compbio.dundee.ac.uk Tue Jan 22 10:43:16 2008 From: tom at compbio.dundee.ac.uk (Tom Walsh) Date: Tue Jan 22 14:21:13 2008 Subject: [Discuss] Re: registration for the tool STAMP (fwd) In-Reply-To: References: <4790E9E6.9030200@compbio.dundee.ac.uk> Message-ID: <4795C8C4.1030202@compbio.dundee.ac.uk> Manickam Muthuraman wrote: > Hi Tom > > I get an error from stamp > error: file dbase.dom does not exist > Use the -d option to specify the database file you're using. The program is obviously reading the name db.dom from the stamp.defaults file. Tom