hi, check it out whether your protein contains any segment name ,since it is missing in alignment file, since 0 residue number in pdb and message of protein not accepted indicates there is a problem in pdb format ,change the format such as ent or pdb and try again and also let me know what happened...(don't use atom format) B.Nataraj
"Chaitanya Reddy.A" chaitanya@msitprogram.net wrote: Dear all, We are modelling a molecule but we are facing a problem to which i am unable to find it. We hope you can help me in this regard. We want to model a map kinase 8 using the map kinase 10 molecule which shows 93% homology. We aligned using clustalx and we submitted to modeller as .ali file.
Below is the alignment file we obtained from clustalx
>P1;1jnk structureX:1jnk:1 : :346 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30 ------DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLA-----SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN------------- ----------------------------------------------------* >P1;output sequence:output:1 : :427 : :JNK mitogen-activated protein kinase:2.40:-1.00:-1.00 MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLEERTKNGVIRGQ PSPLGAAVINGSQHPSSSSSVNDVSSMSTDPTLASDTDSSLEAAAGPLGCCR*
After submitting to modeller, the following is the error..
The error message
rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 346 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Please help me in solving this problem.
But we manually examined the number of residues in both pdb files and alignment files and we found no difference.
Regards Chaitu
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B.Nataraj, Final year M.Tech.(Bioinformatics), SASTRA Deemed University, (www.sastra.edu) Thanjavur, Tamil Nadu, India. Email:nataraj@biotech2.sastra.edu Email:natarajmtech@yahoo.co.uk --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now