Hello all
Now, I normally can do protein-ligand md in gromacs.
But in few cases when I did command:
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh
I got such fatal error:
Using the Amber99sb force field in directory amber99sb.ff
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.r2b
Reading ProteinAmber.pdb...
WARNING: all CONECT records are ignored
Read 'COMPLEX (TRANSFERASE/PEPTIDE)', 807 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 249 residues with 807 atoms
chain #res #atoms
1 'B' 104 807
WARNING: there were 0 atoms with zero occupancy and 807 atoms with
occupancy unequal to one (out of 807 atoms). Check your pdb file.
Opening force field file /usr/share/gromacs/top/amber99sb.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb)
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
Processing chain 1 'B' (807 atoms, 104 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 164 donors and 151 acceptors were found.
There are 228 hydrogen bonds
Will use HISE for residue 204
Will use HISE for residue 236
Will use HISE for residue 242
Identified residue ILE146 as a starting terminus.
Identified residue PRO249 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS188 HIS204 HIS236 CYS241 HIS242
SG334 NE2449 NE2712 SG743 NE2753
HIS204 NE2449 0.599
HIS236 NE2712 2.176 2.448
CYS241 SG743 1.175 1.061 1.618
HIS242 NE2753 1.777 1.709 1.333 0.786
CYS248 SG799 1.284 1.179 2.366 1.444 1.537
Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.arn
Checking for duplicate atoms....
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 114
Fatal error:
Residue 2 named GLN of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I've already read a lot of papers about such problem. But still do not know how to fix that. So,I want to know, how can I fix that error (Can I do that ?)?
I would be very grateful for any assistants.
What that is telling you is that the PDB file you're starting from (the original crystal structure?) does not include all atoms. A very quick and dirty fix is to simply open your file in Swiss PDB Viewer - it will automatically build in missing sidechains.
Perhaps a more important note to keep in mind, though: not all crystal structures are created equal. Why was this atom omitted from the structure? Was it because that sidechain was truly unresolved, or is it a sign of a fitting error? As a starting point I'd suggest you go back to the entry in the PDB and have a look at the fitting stats they provide, paying particular attention to the number of outliers. What resolution was it solved at? Above about 2.5 Angstroms, the likelihood of residual errors of types that will not be fixed by even very long term equilibrium MD become very high. I'm working on a tool that will help with this sort of initial evaluation and refinement of starting structures for MD, but it's not quite ready for prime time.
What that is telling you is that the PDB file you're starting from (the original crystal structure?) does not include all atoms. A very quick and dirty fix is to simply open your file in Swiss PDB Viewer - it will automatically build in missing sidechains.
Perhaps a more important note to keep in mind, though: not all crystal structures are created equal. Why was this atom omitted from the structure? Was it because that sidechain was truly unresolved, or is it a sign of a fitting error? As a starting point I'd suggest you go back to the entry in the PDB and have a look at the fitting stats they provide, paying particular attention to the number of outliers. What resolution was it solved at? Above about 2.5 Angstroms, the likelihood of residual errors of types that will not be fixed by even very long term equilibrium MD become very high. I'm working on a tool that will help with this sort of initial evaluation and refinement of starting structures for MD, but it's not quite ready for prime time.
you need to edit missing residues/chains use external software for this purpose or use -h flg for help (pdb2gmx -h) it will help you.
Thanks everyone. I've already solve the problem.
This answer helped me.
Tristan Croll · 21.99 ·
51.46 · Queensland University of Technology
What that is telling you is that the PDB file you're starting from (the original crystal structure?) does not include all atoms. A very quick and dirty fix is to simply open your file in Swiss PDB Viewer - it will automatically build in missing sidechains.
Perhaps a more important note to keep in mind, though: not all crystal structures are created equal. Why was this atom omitted from the structure? Was it because that sidechain was truly unresolved, or is it a sign of a fitting error? As a starting point I'd suggest you go back to the entry in the PDB and have a look at the fitting stats they provide, paying particular attention to the number of outliers. What resolution was it solved at? Above about 2.5 Angstroms, the likelihood of residual errors of types that will not be fixed by even very long term equilibrium MD become very high. I'm working on a tool that will help with this sort of initial evaluation and refinement of starting structures for MD, but it's not quite ready for prime time.
@Amneh Shtaiwi: download Swiss-PDB Viewer (http://spdbv.vital-it.ch/ - hopefully that link works), open the problematic molecule, then (once it has loaded and SPDB has added the missing bits), go to File > Save > Current Layer (command-S on a Mac) and save the file back to your computer. That new file should have all the missing atoms added and you should be in business.
i also want know how to deal with such problem? other software can edit the missing residue?like pymol or maestro?
@Fan Defang, I've heard that PyMol can do this as well, but I never figured out how and since SPDBV will do it automatically when you import, it seems like the obvious choice just for simplicity's sake.
thanks but I could not use prime software because it is commercial and it does not free.
Thank you very much, although the answer has not been addressed to me. The tool "spdbv" that you offer to fix the resis and missing atoms, really is very good and works perfectly in Win10. I had a good time trying to solve this problem in order to start my MD simulations.
Dear Jonas Powell, I have tried downloading Swiss-PDB Viewer but it is not supported on ubuntu. Is there any other way to do it?
thanks in advance
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