When I try to execute following lines :
mfold SEQ='PDB_00078.fasta' RUN_TYPE=text or mfold SEQ='PDB_00078.fasta' RUN_TYPE=html
I get the following error:
mfold version 3.5
unluckily I also have been unable to install it in the long run as I had different errors (see my different post), so I've given up on local mfold and been using the web server alternatively and additionally the Vienna package.
i am not sure if it's the mfold code itself or something with Ubuntu (i am also using Ubuntu), however I don't have these types of problems with compiling with other software program.
I am not sure why this is not been answered by anybody. But I really could not get rid of this problem. Did any one body found solution ?
auxgen is a minor program in the mfold package that formats the sequence in an easy to read way. However,
auxgen is the first program to be called by the mfold script. If the package is not installed, then the first error to occur will be the failure to find the
auxgen program. Getting this error is an indication that the software is not installed. When setting up mfold, you must first run the "configure" script with the appropriate flags. Then run "make" and finally "make install" to place the executable files and energy files in the right place. If you do not use "--prefix=..." when configuring, then the executable files will be placed in /usr/local/bin when you install, and the energy files will be placed in /usr/local/share/mfold. That is, not using prefix is equivalent to using
To check if mfold is properly installed, issue the command:
echo $PATH|tr ':' '\012'
One of the listed directories must contain
auxgen, nafold, ....; that is, all the executable files in the package. If you do not know how to use configure scripts in Unix/Linux, then ask someone to help you.
For the record, mfold is obsolete. The replacement UNAFold software is both better and easier to install. It may be downloaded from this site.
i am facing the same problem
on Ubuntu: sudo apt-get install gfortran
then rebuild mfold from source (./configure, make, make install) and it will work.