[gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

[Liu Shiyong]

I tried amber99 and amber03. I got the same error info :


Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file /usr/local/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file /usr/local/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file
/usr/local/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file
/usr/local/share/gromacs/top/amber03.ff/aminoacids.c.tdb
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file /usr/local/share/gromacs/top/amber03.ff/dna.arn
Opening force field file /usr/local/share/gromacs/top/amber03.ff/rna.arn

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Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom P in residue G 201 was not found in rtp entry RG5 with 32 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"RTFM" (B. Hess)


Using the Amber03 force field in directory amber03.ff

Reading 1A1T_amber03.pdb...
Read 'SL3 STEM-LOOP RNA; NUCLEOCAPSID PROTEIN', 873 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 3 chains and 0 blocks of water and 57 residues with 873 atoms

  chain  #res #atoms
  1 'B'    20    432
  2 'A'    55    439
  3 'A'     2      2

Reading residue database... (amber03)

Processing chain 1 'B' (432 atoms, 20 residues)
Identified residue G201 as a starting terminus.
Identified residue C220 as a ending terminus.