From the error message that you received,
Save file is empty. No foldings.
Job Aborted
I conclude that the mfold software is not installed properly.
You need to give me information. I assume that you downloaded the mfold software from
http://www.unafold.org/mfold/software/d ... -mfold.php Is that correct. What platform are you running it on? What is in the log file?
In any case, you are using the software incorrectly if you want to fold many sequences at the same time. You need to use the underlying folding program, 'nafold'. This is run interactively. When you run the command: 'nafold', enter '0' at the first prompt for a 'regular run'. For 'run mode', enter '2' for 'Multiple Molecules'. Then enter the sequence file name (FASTA format). Then enter information as it is requested. Allow the default energy rules to be used. If that fails, then you don't have a proper installation. Select Y for 'printer output'. I strongly suggest entering a file name. Enter N (No) for the other two kinds of output, and finally enter '10' for 'begin folding'
For the input file 'rand.seq' below:
>r1
CAGCACGCCGACCAUCGCGUGAGAGAUUCCACUAGGGAUACGAAUCAUUGCCUUGUCGCC;
>r2
CCAACGUGCGGGCAUUGUGACUGCGGUCGUCUCAUAGUGACACGGCAACUGGCGCGCGUU;
>r3
AGGCAAUACUAUCGUCCUAAUCGGGCGGGCAGCCGAAAAAGAUUUCCUUCGAGGCCGGUU;
>r4
GCGAUGGGUCGGCCUCAGAUCGGAUACUUUCUAGGACCGGAAGUCUAGAAGAUUCCUCAU;
>r5
CCGGUCUCAACAAUUACUAUCAAAUUAUGGGAGCCAGCUACUCGGCUGUAAUCGACAUAG;
>r6
CAUCAGCUUAUCGCUAACUUUAACAGUGUCGUUCUCCCUACGAUCAGCGACGACGUCACG;
>r7
UUCUACUGAGCGAACCGCUGCGAAAAUUCCGAAAUAAAUACGUCGGCAGAAUCAAAGAGG;
>r8
CGUUCUGCAUUCACACUUGUUUGGUCGCAAUAUUGAACACACUCUAUUGGGUAUACUUCC;
>r9
AUAUCGAUAACGGACCCUACAAGGUGCUAUACGAUCUACGAUCAAGGGGUAUGGCACCUA;
>ra
GUUCGAGCAAGGGCCUUCUUCUCAACAAUUUCUGAGCGGAUUGCGGAUGGACGGCCCAUC;
>rb
CCCAACUGCCGUACGAACUGAAGACCCGGGGGUAGGGACCCACACCCCCUUAAUCAGGAG;
>rc
GGUGGGAAUUGGUUCCGAAGGAGGCUCAUUCGCUGUUGAAAGGAUGGUUAUACGUCAACG;
>rd
AUCGUAGGGAGAGCGAGGACCUCACCAAGGGACCAAUCCUGGUUAACGGCAAGAUAGCGC;
>re
GUGUUUACAAGAGGGUGAACGUGCGUGCCCAGUCAGCUGGAGACGGAACAAGGGACUUAG;
>rf
GCGACUGCAAUCGUUCGCCGGGUACCAAUAUCAUGCUAAUUAUAUCUAGGGCACUUUGGG;
>rg
AUUGGUAAGCGCUCGUUUUUUACACCCUACGUUUGCUUGAGUGAAUGCAAAUGAGGCCUG;
>rh
GGGAGCCCAUGGCGCCUUCAAGUAACCUACUAAACGCAAUGAAGGGAUUGUUUGCUGUCG;
>ri
AGGUUAAAGCUGUCUCGGGAGGACGCUAUUGCAGGACAACUGAAUCAUUUAUCUAACUCC;
>rj
UUCGCUAAAUUGAUUCCGAGGGAGAAAUUAUAGCCCGGCCGGGCUGUCGUCUAGCGUGCA;
>rk
CUGGUAAUCAAAGACAAUUUCCAUUCAACUGCGUAUGUCCGCGGGUUCGCGACACAUAGC;
the result is
Sequence 1 Structure 1
Folding bases 1 to 61 of r1
dG = -12.50
10 20 30
CAGCACGC CATC - GAG--| A
CGAC GC GTGA ATTCC C
GCTG CG TACT TAGGG T
;CC----- TTC- T AAGCA^ A
60 50 40
Sequence 2 Structure 1
Folding bases 1 to 61 of r2
dG = -20.70
10
CC .-G| TTG
AACGTGCG GCA \
TTGCGCGC CGT T
;- \ -^ CAG
60 20
30
G----- C AT
GTCGT TC \
CGGCA AG A
GGTCAA C TG
50 40
Sequence 3 Structure 1
Folding bases 1 to 61 of r3
dG = -14.40
10
A---- .-AATACTA| TA
GGC TCGTCC \
CCG GGCGGG A
;TTGG \ -------^ CT
60
30 40
GCAGC AAAG
CGAA A
GCTT T
GA--- CCTT
50
Sequence 4 Structure 1
Folding bases 1 to 61 of r4
dG = -12.60
10 20
GC--------------| GGG - C TCGG
GAT TCGG CCT AGA A
CTG GGCC GGA TCT T
;TACTCCTTAGAAGAT^ AA- A - TTCA
60 50 40 30
Sequence 5 Structure 1
Folding bases 1 to 61 of r5
dG = -9.10
10 20
CCG-- .-TCAACAATTA| CA
GTC CTAT A
CAG GGTA A
;GATA \ ----------^ TT
60 30
40
GAGC- A
CAGCT C
GTCGG T
CTAAT C
50
Sequence 6 Structure 1
Folding bases 1 to 61 of r6
dG = -11.80
.-CATC| TT
AGC \
TCG A
\ ----^ CT
20 30 40
AACTTTAACA T C C AC
GTG CGTT TC CT G
CAC GCAG AG GA A
;G-------- T C C CT
60 50
Sequence 7 Structure 1
Folding bases 1 to 61 of r7
dG = -7.20
10
-- .-ACTG| A
TTCT AGCG \
GAGA TCGC A
;G \ ----^ C
60
20 30
GC AAATT AATA
GA CCGA A
CT GGCT A
AA AAGAC GCAT
50 40
Sequence 8 Structure 1
Folding bases 1 to 61 of r8
dG = -8.10
10
.-C -----| AT CAC
GTTC TGC TCA T
CAAG ACG GGT T
\ - TTATA^ CT TTG
30 20
40 50
ACACTCTATT TA
GGG T
CCT A
;--------- TC
60
Sequence 9 Structure 1
Folding bases 1 to 61 of r9
dG = -17.90
.-ATA| A
TCG T
GGC A
\ ---^ A
10
20 30 40
ACCCTACA GA ACG
AGGTGCTATAC TCT \
TCCACGGTATG GGA A
;A------ G- ACT
60 50
Sequence 10 Structure 1
Folding bases 1 to 61 of ra
dG = -19.10
10 20 30
GTTCGAGCAA| T TC AA CT
GGGCC TCT TC CAATTT G
CCCGG AGG AG GTTAGG A
;CTA------^ C T- GC CG
60 50 40
Sequence 11 Structure 1
Folding bases 1 to 61 of rb
dG = -14.20
10 20 30
CCCAACTGCCGTACGAA| AGACCC A- G
CTGA GGGGGT GG \
GACT CCCCCA CC A
;GAG-------------^ AATT-- CA C
60 50 40
Sequence 12 Structure 1
Folding bases 1 to 61 of rc
dG = -11.30
10
TG - T -| G
--GG G GAAT GG TTCC \
TT C CTTA TC GAGG A
\ GT G C G^ A
30 20
40
GAAAG GT
GATG T
CTGC A
;GCAA AT
60 50
Sequence 13 Structure 1
Folding bases 1 to 61 of rd
dG = -10.70
.-A| AGG
TCGT \
AGCG G
\ -^ AGA
10
20 30
.-GGACCTC A AC
ACCA GGG \
TGGT CCT C
\ ------- - AA
40
50
TAACG AA
GC G
CG A
;CG-- AT
60
Sequence 14 Structure 1
Folding bases 1 to 61 of re
dG = -15.50
10
.-G| AA
TGTTTAC G
GCAAGTG A
\ -^ GG
20
30 40
TGC-- G AGTCAG G
GT CCC CTG A
CA GGG GGC G
;GATT - AACAA- A
60 50
Sequence 15 Structure 1
Folding bases 1 to 61 of rf
dG = -8.80
| C C
--GCGA TG A
CGCT GC A
\ ^ T T
10
20 30 40
CGGGTA TATCA AATTA
CCAA TGCT T
GGTT ACGG A
;G---- TC--- GATCT
60 50
Sequence 16 Structure 1
Folding bases 1 to 61 of rg
dG = -11.10
10
.-ATTG ---| G
GTAA GC C
CATT TG T
\ ---- TTT^ C
20
30 40
AC--- A TTGA
CCT CGTTTGC G
GGA GTAAACG T
;GTCC - TAAG
60 50
Sequence 17 Structure 1
Folding bases 1 to 61 of rh
dG = -12.50
10 20
-- G CC TG CG --------| A
GG AGC A G CCTTCA AGTA \
CT TCG T T GGAAGT TCAT C
;G G TT GT AG AACGCAAA^ C
60 50 40 30
Sequence 18 Structure 1
Folding bases 1 to 61 of ri
dG = -11.00
10
A-- .-A| T T G
GGTTA AGC GTC C G
TCAAT TCG CAG G G
;CC \ -^ - - A
60 20
30
ATTG------- GA
CAG \
GTC C
CTATTTACTAA AA
50 40
Sequence 19 Structure 1
Folding bases 1 to 61 of rj
dG = -17.60
10
TT--- .-AATTGA| G
CGCTA TTCC \
GCGAT GAGG A
;ACGT \ ------^ G
60 20
30
AAATT G
ATAGCCC G
TGTCGGG C
CTGC- C
50 40
Sequence 20 Structure 1
Folding bases 1 to 61 of rk
dG = -10.30
10
.-C| T CAA
TGG AAT A
ACC TTA G
\ -^ T ACA
20
30 40
TTCAACT G C- G
GC TATGT CGCG G
CG ATACA GCGC T
;------ - CA T
60 50
I strongly suggest that you read the manual at:
http://www.unafold.org/doc/mfold-manual/ (you can download a pdf version).
What sort of output are you looking for?
It would be much easier for you to install the UNAFold software.