Recommendations for the compilation of MSAs
Alternatively you may consider a precompiled MSA as e.g. offered by the HSSP-database, which is also accessible via ftp-server. For the conversion of HSSP-files into multiple FASTA format, we recommend STRAP which is available as a Java-Webstart application.
Simply load a HSSP-file, select the sequences related to the proper chain (sequence names composed like A_ for chain A) and export the alignment in FASTA-format, which can be chosen as a format with the Export alignment ... options.
If you want to use the lastest beta-version of STRAP download the program:
wget -N http://www.bioinformatics.org/strap/betaStrap.jar
You may also use the following code to convert a HSSP-file to a multiple FASTA File. Note that a HSSP file may contain sequences from more than one chain, which have to be separated to constitute different MSAs:
java -jar betaStrap.jar -toFasta=1gpw.mfa 1gpw.hssp