RNA Ligand Simulation Problem

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1

GROMACS version: 2020
GROMACS modification: No
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I want to make an RNA-ligand Simulation for 10ns. the RNA residues were in one-letter code rather than 3 letters ( U instead of URA). the Gromacs all-atom forcefield can only recognize the 3-letter code. however somehow managed to change the residues 1 letter code to 3 letters, but the problem I faced after running “gmx pdb2gmx -f [RNA]_clean.pdb -o [RNA]_processed.gro -ter”. I have chosen the options for 5ter and 3ter and they generate error messages.
“Atom OP1 in residue URA 3 was not found in rtp entry URA with 28 atoms while sorting atoms.”
I also tried to use different terminal options but still did not work with none of them.

2

Hi @mahir .

I am not sure I can help you fix the problem but I might be able to diagnose it better and thus get more knowledgeable people to contribute a fix.

Please display at least a portion of the .pdb where an offending URA is described.

For example,

grep ' URA ' [RNA]_clean.pdb | head -n 20

Then, compare it to the .rtp file of your forcefield.

For example, in charmm36_ljpme-jul2022.ff/na.rtp you can see

[ URA ]
; O4
  [ atoms ]
        P        P  1.5000   0
      O1P      ON3 -0.7800   0
      O2P      ON3 -0.7800   0
      O5'      ON2 -0.5700   0
      C5'     CN8B -0.0800   0
      H5'      HN8  0.0900   0
     H5''      HN8  0.0900   0
      C4'      CN7  0.1600   1
      H4'      HN7  0.0900   1
      O4'     ON6B -0.5000   1
      C1'     CN7B  0.1600   1
      H1'      HN7  0.0900   1
       N1     NN2B -0.3400   2
       C6      CN3  0.2000   2
       H6      HN3  0.1400   2
       C2     CN1T  0.5500   2
       O2      ON1 -0.4500   2
       N3     NN2U -0.4600   2
       H3      HN2  0.3600   2
       C4      CN1  0.5300   2
       O4      ON1 -0.4800   2
       C5      CN3 -0.1500   2
       H5      HN3  0.1000   2
      C2'     CN7B  0.1400   3
     H2''      HN7  0.0900   3
      O2'      ON5 -0.6600   3
      H2'      HN5  0.4300   3
      C3'      CN7  0.0100   4
      H3'      HN7  0.0900   4
      O3'      ON2 -0.5700   4
  [ bonds ]
        P   O1P
        P   O2P
        P   O5'
      O5'   C5'
      C5'   C4'
      C4'   O4'
      C4'   C3'
      O4'   C1'
      C1'    N1
      C1'   C2'
       N1    C2
       N1    C6
       C2    N3
       N3    H3
       N3    C4
       C4    C5
      C2'   C3'
      C3'   O3'
      O3'    +P
      C2'   O2'
      O2'   H2'
      C1'   H1'
      C2'  H2''
      C3'   H3'
      C4'   H4'
      C5'   H5'
      C5'  H5''
       C5    H5
       C6    H6
       C2    O2
       C4    O4
       C5    C6
  [ impropers ]
       C2    N1    N3    O2
       C4    N3    C5    O4

It might also be useful to report to this forum, for example, the corresponding entry in the content of the charmm36_ljpme-jul2022.ff/na.hdb file.

URA        10
1       6       H5'     C5'     C4'     O5'    
1       6       H5''    C5'     O5'     C4'    
1       5       H4'     C4'     C3'     C5'     O4'    
1       5       H1'     C1'     C2'     N1      O4'    
1       1       H6      C6      C5      N1     
1       1       H3      N3      C2      C4     
1       1       H5      C5      C4      C6     
1       5       H2''    C2'     C1'     C3'     O2'    
1       2       H2'     O2'     C2'     C1'    
1       5       H3'     C3'     C2'     C4'     O3'

Finally, you might want to look at your /usr/local/gromacs/share/gromacs/top/residuetypes.dat file. Blame it on my ignorance but I would have expected to see an entry like this:

URA RNA

however, my installation (2024.1) shows this:

U RNA

My understanding is that all those atom names MUST match if you are to hope for pdb2gmx execution that does fail.

I hope that someone will add a contribution to actually solve your problem.

Ivan