i am trying to solvate and neutralize a system containing more than 99,999 atoms (in my system an atom forms one residue) using VMD. however when i try to use psfgen to generate a segment for it, it only reads the first 10,000 atoms (residues) only.
attached is a file of the system.
How can i solve this problem?
In the standard PDB format, columns 7 to 11 are reserved for atom number, hence the largest allowable number is 99999. Split the PDB file into segments (chains) of no more than 99,999 atoms and number atoms in each segment from 1.
Martin Klvana i renumered the atoms as you suggested but it now produces an error saying that there is a duplicate residue key. the residue numbers start from 1 to 9999 then repeat again from 1 and so on.
Ibrahim M. Ibrahim
Is now each segment assigned a unique chain identifier (column 22; e.g., A, B, C, etc.)?
Martin Klvana
yes the first 99,999 atom are named A while the rest (less than 99,999) are named B
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