[gmx-users] How to solve OXT atom (termial oxygen atom) issue?
palusoori at gmail.com
Fri Dec 16 06:33:16 CET 2016
First of all I am extremely sorry for my mistake. I haven't sent you the
modified coordinate file.
I have peptide with 69 residues and some of the SER and THR residues
are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
and 69) have been modeled by modeller . I have chosen charmm36 force field.
When I executed the command
pdb2gmx -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh
I got following error.
Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15
atoms while sorting atoms.
I have checked the rtp file and it does not have the terminal oxygen
atom GLN. Then I have checked c.tdb file and I found the following
[ None ]
; CHARMM CTER
[ COO- ]
[ replace ]
C C CC 12.011 0.34
O OT1 OC 15.9994 -0.67
OXT OT2 OC 15.9994 -0.67
[ add ]
2 8 OT C CA N
OC 15.9994 -0.67 -1
[ impropers ]
C CA OT2 OT1
What I understand here is that the OXT atom is to be replaced by OT2
and add the information to the rtp file. Am I right?
Internally, pdb2gmx re-maps any reference to the OXT atom to one named
OT2. No changes are made to the .rtp file and you certainly don't need to
Please upload your coordinate file somewhere and provide a URL. I cannot
reproduce the problem with a simple test system. A peptide that I have
with a C-terminal GLN works fine with either O/OXT or OT1/OT2.
As Justin asked me coordinate file, I have provided below the link of my
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