I am trying pdb2gmx command for MD simulation. but the output of pdb2gmx is not working properly in-case of multiple chains. the output file of pdb2gmx >>> .pdb or .gro was not generated.
ERROR MSG:
WARNING: atom HH21 is missing in residue ARG 215 in the pdb file
You might need to add atom HH21 to the hydrogen database of building block ARG
in the file aminoacids.hdb (see the manual)
WARNING: atom HH22 is missing in residue ARG 215 in the pdb file
You might need to add atom HH22 to the hydrogen database of building block ARG
in the file aminoacids.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.5.6
Source code file: pdb2top.c, line: 1489
Fatal error:
There were 30 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"It is Lunchtime" (A.R. Van Buuren)
Using the Gromos43a1 force field in directory gromos43a1.ff
Reading 3.pdb...
Read ' KINASE', 1711 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 1 blocks of water and 571 residues with 1711 atoms
chain #res #atoms
1 'A' 227 1670
2 ' ' 41 41 (only water)
Reading residue database... (gromos43a1)
Processing chain 1 'A' (1670 atoms, 227 residues)
Identified residue LEU27 as a starting terminus.
Identified residue THR261 as a ending terminus.
Start terminus LEU-27: NH3+
End terminus THR-261: COO-
Checking for duplicate atoms....
Now there are 1666 atoms. Deleted 4 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 227 residues with 2086 atoms
Hi,
You should try to add the "-ignh" flag to the pdb2gmx command line. This flag tells pdb2gmx to ignore the H atoms in your input.
Best,
A.
Dear nitin,
You must Simply set the " -missing " flag to the pdb2gmx command line.
HAH
thanks for your suggestions............
but i have problem with multiple chains in a single protein molecule. in this case pdb2gmx generates itp fileswith different chains but not generate GROMACS comfortable co-ordinate file (.pdb or .gro).
Dear Nitin,
I don't understand what you exactly mean?
If you have problem with multiple chains you must edit your pdb file with a text editor and remove extra chains before starting pdb2gmx.otherwise send your pdb file to my email ([email protected]).I will make your necessary files.
best
HAH
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