My .pdb file is of a solvated ATP. I was trying to change the (res)name in the .pdb TIP3W to TIP using atomselect in tcl. But something is not working. I am confused how to select "TIP3W". I guess its similar to resname for proteins. I have attached the script I used for doing so and the pdb file.
Could anyone help me in this. The .pdb file is found to contain format errors due to the absence of a space after (res)name 'TIP3W' from ATOM 446 onwards. I would really appreciate any other practical suggestions to overcome this format issues.
Thanking you in advance,
Krithika.
Hello Krithika
try
set all [atomselect top "all"]
set a [atomselect top water]
$a set resname TIP
$all writepdb 123.pdb
Your residue name is not TIP3W, the W is the chain identifier.
PDB format specifies characters 18 - 20 as the Residue name
and character 22 is the chain ID.
Character 21 should be a space and different software will treat a non-space here differently.
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
You can just use Notepad++, where you can select the entire TIP3 and then you can change it to TIP
Matthew James Conroy Thank you ! That was a relevant observation I should have noticed. Thank you for helping me out.
Aashish Bhatt Kiran Lokhande Thank you for the suggestions. I was able to edit my .pdb using them to a new one with correct format.
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