I'm doing something wrong, I'm a novice though, so I know what what. I'm using a fairly simple TOP script to generate a model a nitroreductase. I've used blast on NCBI to find a simialr protein to the one I have the pdb model for. The blast results look like this :
Query: 1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV Sbjct: 1 MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60
Query: 61 AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120 AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG Sbjct: 61 AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120
Query: 121 RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180 R +FADMHR DL DD +WMAKQVYLNVGNF PIEGFDAAILD EFGLKE Sbjct: 121 RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180
Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216 KG+TSLVVVPVGHHSVEDFNATLPKSRLP + +TE Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216
How do I then transform this into a successful alignment file? My attempt looks something like this: >P1;1OO5 structureX:1OO5: 2 :A: 217 :D:undefined:undefined:-1.00:-1.00 mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfnerkml dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnvgnfll gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev*
>P1;1NEC sequence:1NEC: 2 :A: 216 :D:undefined:undefined:-1.00:-1.00 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKML DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFL LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE*
I've basically taken the Query sequence (1OO5) which I have the pdb file for and placed it in the sequence section, then taken the result sequence which has been matched to it (1NEC) and placed it in the second position of the alignment file with the sequence label. However, when I run it, in my mod.log file, I'm getting the error:
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 5377489 5251.454 5.128 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali read_al_375E> Unknown residue type,position,sequence: m 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
As far as I can gatherThis means that it doesn't like the residue at position one. I don't however know what it doesn't like about the residue at that position. Am I creating the alignment file in the wrong manner? Is there something else wrong?
In case it of any use, the top file looks like: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '1ICV.ali' # alignment filename SET KNOWNS = '1ICV' # codes of the templates SET SEQUENCE = '1NEC' # code of the target # SET HYDROGEN_IO = on SET HETATM_IO = on SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate) SET PDB_EXT = '.modlr.pdb' SET MD_LEVEL = 'refine_5' SET LIBRARY_SCHEDULE = 1 CALL ROUTINE = 'model
Thanks. Ben.
You should convert your sequence (1005) to upper case. MODELLER interprets some of the smaller case single-letter residue codes as other residues (see $LIBS/restyp.lib).
Eswar.
On Oct 13, 2004, at 5:19 AM, bcur001@ec.auckland.ac.nz wrote:
> I'm doing something wrong, I'm a novice though, so I know what what. > I'm using a fairly simple TOP script to generate a model a > nitroreductase. > I've used blast on NCBI to find a simialr protein to the one I have > the pdb > model for. The blast results look like this : > > Query: 1 > MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 > MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV > Sbjct: 1 > MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 > > Query: 61 > AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120 > AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG > Sbjct: 61 > AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120 > > Query: 121 > RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180 > R +FADMHR DL DD +WMAKQVYLNVGNF PIEGFDAAILD EFGLKE > Sbjct: 121 > RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180 > > Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216 > KG+TSLVVVPVGHHSVEDFNATLPKSRLP + +TE > Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216 > > > How do I then transform this into a successful alignment file? > My attempt looks something like this: >> P1;1OO5 > structureX:1OO5: 2 :A: 217 :D:undefined:undefined:-1.00:-1.00 > mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfn > erkml > dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnv > gnfll > gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev* > >> P1;1NEC > sequence:1NEC: 2 :A: 216 :D:undefined:undefined:-1.00:-1.00 > DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNE > RKML > DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNV > GNFL > LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE* > > I've basically taken the Query sequence (1OO5) which I have the pdb > file for and > placed it in the sequence section, then taken the result sequence > which has > been matched to it (1NEC) and placed it in the second position of the > alignment > file with the sequence label. > However, when I run it, in my mod.log file, I'm getting the error: > > Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 > 2153.583 2.103 > openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali > > Dynamically allocated memory at amaxbnd [B,kB,MB]: 5377489 > 5251.454 5.128 > openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali > read_al_375E> Unknown residue type,position,sequence: m 1 > 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > As far as I can gatherThis means that it doesn't like the residue at > position > one. I don't however know what it doesn't like about the residue at > that > position. Am I creating the alignment file in the wrong manner? Is > there > something else wrong? > > In case it of any use, the top file looks like: > INCLUDE # Include the predefined TOP > routines > SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log > file > SET ALNFILE = '1ICV.ali' # alignment filename > SET KNOWNS = '1ICV' # codes of the templates > SET SEQUENCE = '1NEC' # code of the target > # SET HYDROGEN_IO = on > SET HETATM_IO = on > SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 10 # index of the last model > # (determines how many models to > calculate) > SET PDB_EXT = '.modlr.pdb' > SET MD_LEVEL = 'refine_5' > SET LIBRARY_SCHEDULE = 1 > CALL ROUTINE = 'model > > > Thanks. > Ben. > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage
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bcur001＠ec.auckland.ac.nz -
Eswar Narayanan