I am working on molecular dynamics simulation of a protein structure with
approximately 1900 residues.
In PDB, only c-alpha trace was available for this protein.
I generated full-atom model using the following steps:
After these 3 steps, I assessed the quality of the structure using
PROCHECK via PDBSum and noticed that approximately 3% of the residues are in the
disallowed region.
I would like to know the best practice to fix the
residues in disallowed region ? Is there any tool or methodology (for
example energy minimization) that can adjust the phi-psi values of
residues in disallowed region ? I would also like to know if there is any
better equivalent for the tools that I have used for side-chain atom
generation and fixing the missing atoms.
I am generating by hand some PDB structures that only contain alpha carbons, but when I submit them to maxsprout I always get the error "No atom chains found, invalid input file?", what could be the reason? Or, could you paste here somehow files you submitted to maxsprout and which only contain alpha carbons? thankis a lot
I once was told that you are likely to make things worse if you start with EM here (haven't done anything myself in years).
How many residues in regular protein structure are in disallowed (or energetically unfavorable) states? 3% does not seem out of this world. Depending on your overall goal, you could leave it as is and proceed with MD. If you have a specific question regarding the molecule it could be answered irrespective of it.
Roland thanks a lot for your thoughts. I have 32 residues and most of them are in the loop regions. The overall aim is to map a nsSNP identified in a GWAS to this structure and study the conformational changes induced by the mutation.
Roland: thanks a lot for your thoughts. I have 32 residues and most of them are in the loop regions. The overall aim is to map a nsSNP identified in a GWAS to this structure and study the conformational changes induced by the mutation
In Deep view itself you can push this amino acids into the core region by building a loop between above and below amino acids of your target amino acid which is in disallowed region. just follow the below steps.
Open your given pdb file in Deep viewer.
Go to control panel and color all amino acid in to any single color.i will suggest you to give pink color to the whole structure.
Give any particular color for your target amino acid which is in disallowed region and two amino acids below and two amino acids above of your target amino acid you give some different color.
For example: following are your amino acids in your pdb - 34LYS,35His,36Arg,37Ile,38Pro,etc. say for instance. 36th Arg is in disallowed region. you change the color of 36th Arg into Green color. and 34th and 35th you give red Color. 37th and 38th you give Blue color.
Now you see Ramachandran plot once again and confirm that green color amino acid is in disallowed region. Once you confirm you can build a loop.after confirmation you may close ramachandran plot.
Go to Build menu. select "Build loop".now you can see click on 1st anger.
Now you click on any anger of 34th or 35th amino acid and then it will ask you click on second anger this time you may click on 37th and 38th amino acid. Immediately confirmation and geometry will change. now you can see the green amino acid will be inside the core region.
Once you done with this you may perform Energy Minimization. then you can save the structure.
I am generating by hand some PDB structures that only contain alpha carbons, but when I submit them to maxsprout I always get the error "No atom chains found, invalid input file?", what could be the reason? Or, could you paste here somehow files you submitted to maxsprout and which only contain alpha carbons? thankis a lot