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

[Justin A. Lemkul]

Liu Shiyong wrote:
> 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
> 
> -------------------------------------------------------
> 
> 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
> -------------------------------------------------------
> 

The .rtp entry defines which atoms should be present in the residue.  If you 
look at rna.rtp, you will find what is expected.  The RG5 definition does not 
include a 5' phosphate, but likely your structure does.  You must supply a 
structure that conforms to the expectations of the force field.

Also note that the solutions to just about all the errors you will face can be 
found on the Gromacs website or in the mailing list archive.  For instance:

http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

-Justin

> "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.

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================