From: Thierry Oscar Wambo (
Date: Fri Sep 26 2014 - 08:04:18 CDT

Good morning everyone!

I have been trying to phosphorylate a SER residue on a protein. I build the psf and pdb files using the script at the bottom. but while the script was running, I received warnings that some explicits angles in residues TIP3 will be deleted. The bottom line is that when I open the above files in vmd some water molecules appear in a shape of a closed triangle.

the warning messages are attached to this email.

Please, can you look at the warning messages and help me to fix this issue?

Thank you in advance.


topology topology/top_all27_prot_na.rtf
topology topology/par_all27_prot_na.prm
topology topology/stream/toppar_prot_na_all.str
pdbalias atom ILE CD1 CD
pdbalias atom GLY OXT OT1
pdbalias residue HIS HSE
pdbalias residue HOH TIP3
pdbalias atom TIP3 O OH2
segment P1 { pdb chaina.pdb
patch SP2 P1:6
regenerate angles dihedrals
coordpdb chaina.pdb P1
writepdb chain1.pdb
writepsf chain1.psf

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