Zhanglab forum

Hi The issue major occurs after this step "$blastdir/blastpgp -b 1000 -j 3 -h 0.001 -d $db -i protein.fasta -C psitmp.chk -Q pssm.txt > blast.out" you can add the command before this line print "$blastdir/blastpgp -b 1000 -j 3 -h 0.001 -d $db -i protein.fasta -C psitmp.chk -Q pssm.txt...

I-TASSER can not predict the structure after PTM. PTM major occurs on the side-chain, the conformation may not change that much before and after PTM, thus maybe you can first predict the structure by I-TASSER, then modify the side-chain manually based on the PTM sites and type.

Hi Jed, can you do ls to "/home/yourname/ITLIB/nr/nr" see if this file exist? (please replace "yourname as the real place of you, to make the conversation easily, can you tell us the real path next time? The issue you have is the script try to find the /home/yourname/ITLIB/nr/nr file ...

Hi We found two jobs submitted by the email you mentioned, you can find those two at https://zhanggroup.org/C-QUARK/output/QB1515/ and https://zhanggroup.org/C-QUARK/output/QB1522/. Sometime we found some email domain block our email notification (the email administer may block our email domain), ou...

Hi

Have you replace "yourname" in /home/yourname/ITLIB by real place? and please do 'ls" to your ITLIB path and let us check what exists in your folder

Best
IT team

Yes, I think docking or MD need H atoms, but those pipeline actually has the program let you add H atoms, what you need to do is following their tutorial I guess, for example Gromacs etc.

Hi Hydrogen atoms is not essential atom for pdb file, even in experimental structure in PDB database, nearly all structure don't contain hydrogen atoms, so you do not need do anything to the predict structure. And most of the program that you use after structure prediction, like function prediction ...

You can install gfortran (windows) version then use it complies the TM-align program, or you can install WSL in window 10 system. You can find the WSL tutorial from google easily, WSL actually is the linux system.

BTW, it seems you use window subsystem, if I am correct, the java in the WSL system has some issue with the memory, you can try a native linux system instead of WSL if you don't know how to deal with the WSL issue.

Dear user,

It seems the wMUSTER threading failed, please re-try this step until you get the results. Based on the error message, it perhaps your java machine memory is too small,you can try increase it.

Best
Wei