Hi, I also shared same problems. I have changed my phosphorylated residue THR 337, 338, 339, 340 and SER 342 into THP1 and SP1.
PDB2GMX result :
Warning: Residue THP1337 in chain has different type (‘Other’) from
residue ASN1 (‘Protein’). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add THP1 to residuetypes.dat
if this was not correct.
Warning: Residue THP1338 in chain has different type (‘Other’) from
residue ASN1 (‘Protein’). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add THP1 to residuetypes.dat
if this was not correct.
Warning: Residue THP1339 in chain has different type (‘Other’) from
residue ASN1 (‘Protein’). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add THP1 to residuetypes.dat
if this was not correct.
Warning: Residue THP1340 in chain has different type (‘Other’) from
residue ASN1 (‘Protein’). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add THP1 to residuetypes.dat
if this was not correct.
Warning: Residue PHE341 in chain has different type (‘Protein’) from
residue ASN1 (‘Protein’). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add PHE to residuetypes.dat
if this was not correct.
Hence, I have already input residuetypes.dat into my workfiles, and do the pdb2gmx again.
gmx_mpi pdb2gmx -f step5_input.pdb -o CCL19_CCR7active_BARR2_g.pdb -p topology.top -ter
But another warning showing out :
Warning: Starting residue GLY1 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add GLY to residuetypes.dat if this was not correct.
Warning: Starting residue THR2 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add THR to residuetypes.dat if this was not correct.
Warning: Starting residue ASN3 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add ASN to residuetypes.dat if this was not correct.
Warning: Starting residue ASP4 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add ASP to residuetypes.dat if this was not correct.
Warning: Starting residue ALA5 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add ALA to residuetypes.dat if this was not correct.
Disabling further warnings about unidentified residues at start of chain.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS8 CYS9 CYS34 CYS50
SG94 SG104 SG517 SG781
CYS9 SG104 0.756
CYS34 SG517 0.203 0.708
CYS50 SG781 0.900 0.204 0.815
MET72 SD1150 2.970 2.597 2.910 2.485
Linking CYS-8 SG-94 and CYS-34 SG-517…
Linking CYS-9 SG-104 and CYS-50 SG-781…
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Program: gmx pdb2gmx, version 2018.6
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
Fatal error:
Atom HT1 in residue GLY 1 was not found in rtp entry GLY with 7 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.