I am trying to use the Interface alignment option of MM-align.
According to the help section, we can run it using the command:
MMalign complex1.pdb complex2.pdb -I 10
Here's some output I get:
1> MMalign 1avwA-1avwB_1.pdb i12e80L0H ( I think this is fine)
bash-3.2$ MMalign 1avwA-1avwB_1. pdb i12e80L0H
**************************************************************************
* MM-align *
* Aligning protein complex structure by Dynamic Programming *
* Comments on the program, please email to: zhng@umich.edu *
**************************************************************************
Protein 1:1avwA-1avw Size= 394
Protein 2:i12e80L0H Size= 300 (TM-score is normalized by 300)
Aligned length= 95, RMSD= 6.75, TM-score=0.18691, ID=0.028
-------- rotation matrix to rotate Chain-1 to Chain-2 ------
i t(i) u(i,1) u(i,2) u(i,3)
1 87.5244713724 -0.6021981553 0.5981944818 -0.5286972136
2 72.6880642721 -0.2087133496 -0.7571725777 -0.6189736870
3 0.5135653513 -0.7705816760 -0.2623986462 0.5808191036
(":" denotes the residue pairs of distance < 5.0 Angstrom)
ivggytcaansipyqvslnsgshfcggslinsqwvvsaahcyksriqvrlgehnidvlegneqfinaakiithpnfngntldndimliklsspatlnsrvatvslprscaaagteclisgwgntkssgssypsllqclkapvlsdssck-----ssypgqitgnmicvgfleggkdscqgdsggp-------vvcngqlqgivs-wgygcaq---knkpgvytkvcnyvnwiqqtiaan-----------------------------------------------------DFVL------------------------------------------DN------------EGNPLE--------------------N-------------GGTYYILSDITAFGGIRAAPTGNERCPLTVVQSRNELDKGIGTIISSPYRIRFIAEGHPLSLKFDSFAVIMLCVGIPTEWSVV-----------------------EDLPE----GP-AVKIGE-NKDAMDGWFRLERVSEFNNYKLVFCPQDKCGDIGISIDHDDGTRRL------------VVSKNKPLVVQFQKLD--------
. :.. . .:. .. .: ::::::... .. ..:. : :::: :: : .::.... ..... . . ..::.. . ..::: : : . . .:. .:..:::::::.::: .:::::::: ...
d--ivm----------t-----qsq--------------kf----------------------------------------------------------------------------ca-----------------qnvgtavaw-yq-qkpgqspkl--m----iysa----------------snrytgvsg-------f--adyfcqqyssypltfg-------------------agtkeraaptvsifppsseqltsggasvvcflnnfykivwrqngvlnsatdqds---kdstysmsstltltkyehnsytcivksfnrnecDIVMTQSQKF-CAQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVSGFADYFCQQYSSYPLTFGAGTK-E--R-------------------------------------------------------------------------AAPTVSIFPPSSEQLTSGGASVVC----FLNNF-YKIV---WRQNGVLNSATDQDSK---DSTYSMSST-------------------LTLTKYEHNSYTCIV-------------KSFNRNEC
(Odd no chains of both proteins are in lower case and Even no chains of both proteins are in UPPER case)
2> MMalign 1avwA-1avwB_1.pdb i12e80L0H -I 5 (Fortran error)
> bash-3.2$ MMalign 1avwA-1avwB_1.pdb i12e80L0H -I 5 5
**************************************************************************
* MM-align *
* Aligning protein complex structure by Dynamic Programming *
* Comments on the program, please email to: zhng@umich.edu *
**************************************************************************
Protein 1:1avwA-1avw Size= 394
Protein 2:i12e80L0H Size= 300 (TM-score is normalized by 300)
No. Of Interface Residue: Protein 1,Chain 1 : 10 | Protein 1,Chain 2 : 10
Protein 2,Chain 1 : 150 | Protein 2,Chain 2 : 150
Aligned length= 98, RMSD= 7.01, TM-score=0.17622, ID=0.034
-------- rotation matrix to rotate Chain-1 to Chain-2 ------
i t(i) u(i,1) u(i,2) u(i,3)
1 74.4131948023 -0.6363235395 0.6836670796 0.3573397226
2 93.6572286061 -0.7435471571 -0.4201613603 -0.5201942489
3 -28.1979387003 -0.2054993390 -0.5967107805 0.7756972774
At line 872 of file MMalign.f
Fortran runtime error: No such file or directory
Is it normal to get an output like this when we use Interface alignment option?
Can you help me with the problem?
Thank you.