Adding SEP parameter to AMBER99SB.ff

Manvi · April 22, 2021, 4:00am

Hi,
I have to run the simulation for a system containing protein and phosphopeptide complex. I am getting error while converting pdb file to gro format. I have done following modifications:

added SEP parameter to the aminoacids.rtp file

[ SEP ]
[ atoms ]
N N -0.493700 1
H H 0.301800 2
CA CT -0.238000 3
HA H1 0.093700 4
CB CT 0.078200 5
HB2 H1 -0.060200 6
HB3 H1 -0.060200 7
OG OS -0.559300 8
P P 1.4 9
O1P O2 -0.850 10
O2P O2 -0.850 11
O3P O2 -0.850 12
C C 0.673100 13
O O -0.585400 14
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB2
CB HB3
CB OG
OG PS
P O1P
P O2P
P O3P
C O
-C N
[ impropers ]
-C CA N H
CA +N C O

added SEP as protein in residutypes.dat file
added SEP parameter in aminoacids.hdb

SEP 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB2 CB CA OG

After this, I ran the command but getting the following error:

Fatal error:
Atom HB21 not found in rtp database in residue SEP, it looks a bit like HB2

input PDB file:

ATOM 3830 N SEP B 253 173.848 78.352 17.447 1.00 20.02 N
ATOM 3831 CA SEP B 253 174.518 79.224 18.412 1.00 17.19 C
ATOM 3832 CB SEP B 253 174.400 80.676 17.912 1.00 16.67 C
ATOM 3833 OG SEP B 253 173.031 81.042 17.849 1.00 14.04 O
ATOM 3834 C SEP B 253 173.921 79.047 19.823 1.00 19.69 C
ATOM 3835 O SEP B 253 173.093 78.163 20.051 1.00 18.49 O
ATOM 3836 P SEP B 253 172.732 82.584 17.426 1.00 15.24 P
ATOM 3837 O1P SEP B 253 173.084 82.707 15.961 1.00 14.05 O
ATOM 3838 O2P SEP B 253 171.253 82.784 17.678 1.00 13.37 O1-
ATOM 3839 O3P SEP B 253 173.594 83.474 18.291 1.00 15.07 O1-
ATOM 3840 H SEP B 253 172.862 78.535 17.306 1.00 0.00 H
ATOM 3841 HA SEP B 253 175.578 78.974 18.479 1.00 0.00 H
ATOM 3842 HB3 SEP B 253 174.851 80.770 16.923 1.00 0.00 H
ATOM 3843 HB2 SEP B 253 174.948 81.350 18.569 1.00 0.00 H

there is no HB21 in the input file

I wanted to know where I am doing a mistake and how to resolve this.

Manvi · April 22, 2021, 9:34am

I fixed it.
Thanks

s_llabres · April 22, 2021, 12:36pm

Dear Manvi,

I am facing the same problem with a modified histidine. Could you share how you fixed it?

Thanks,

Salome

jalemkul · April 22, 2021, 12:37pm

For the sake of the forum, posting your solution is helpful to the rest of the community. I’d wager that your issue was in the incorrect .hdb line:

because that tells pdb2gmx to add two atoms, HB21 and HB22, to the structure. Once added, they’re not found in the .rtp entry and trigger a fatal error. The optimal solution (in my mind) is to rename the beta hydrogens as HB1 and HB2 in the .rtp entry and set the following .hdb line to generate them (if needed):

2 6 HB CB CA OG

jalemkul · April 22, 2021, 12:47pm

I posted the solution here and on your thread.

Manvi · April 22, 2021, 1:38pm

I did the same Sir.
Thank you.

Manvi · April 22, 2021, 1:57pm

Dear Salome,
This is how I fixed it:

a) copied amber99sb.ff folder to local folder and also copied residuetypes.dat to the local folder
b) added SEP parameter in the aminoacids.rtp:

[ SEP ]
[ atoms ]
N N -0.493700 1
H H 0.301800 2
CA CT -0.238000 3
HA H1 0.093700 4
CB CT 0.078200 5
HB1 H1 -0.060200 6
HB2 H1 -0.060200 7
OG OS -0.559300 8
P P 1.4 9
O1P O2 -0.850 10
O2P O2 -0.850 11
O3P O2 -0.850 12
C C 0.673100 13
O O -0.585400 14
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG PS
P O1P
P O2P
P O3P
C O
-C N
[ impropers ]
-C CA N H
CA +N C O

c) added SEP as protein in residuestypes.dat

SEP Protein

d) added SEP parameter in aminoacids.hdb

SEP 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA OG

after running pdb2gmx command

got fatal error
Fatal error:
Atom HB1 not found in rtp database in residue SEP, it looks a bit like HB2

just renamed
HB2 to HB1
HB3 to HB2 in aminoacids.rtp

and it worked…

Manvi · April 26, 2021, 7:56am

Hi,
Got another issue.
After running EM, the bond between OG and P is broken for SEP.

jalemkul · April 26, 2021, 8:20am

Your .rtp entry has a typo. You try to define a bond between OG and PS (which doesn’t exist) so that bond is not generated, and you’ll be missing several angles and dihedrals, as well. Correct the typo and regenerate the topology.

Manvi · April 26, 2021, 8:34am

I had changed it to OG and P. After that also same issue.

Manvi · April 26, 2021, 8:36am

I got your answer.
I should redo the whole process.

Manvi · May 3, 2021, 7:54am

Hi,
I ran a simulation of a dimeric system where each monomer binds to a peptide.
queries:

ran gmx_mpi rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns and gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns
plotted both the graphs together but the output overlays
how to fix this?
can I plot rmsf for proteins and peptides separately
Thanks

bjwiley23 · July 15, 2022, 8:35am

I am having reverse issue. The correct naming PDBv3 hydrogen naming convention that pdb2pqr and pdbfixer both use indicates for MET (and many other residues) that HB2 and HB3 should be used over HB1 and HB2. See https://files.rcsb.org/ligands/view/MET.cif. Same thing goes for the gamma carbon hydrogens. How do I make sure the .rtp and .hdb file are in sync to do this? With only updating the .rtp as in:

[ MET ]
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_224B   0.140     1
    HA    opls_140    0.060     1
    CB    opls_136   -0.120     2
   HB2    opls_140    0.060     2
   HB3    opls_140    0.060     2
    CG    opls_210    0.048     3
   HG2    opls_140    0.060     3
   HG3    opls_140    0.060     3
    SD    opls_202   -0.335     4
    CE    opls_209   -0.013     5
   HE1    opls_140    0.060     5
   HE2    opls_140    0.060     5
   HE3    opls_140    0.060     5
     C    opls_235    0.500     6
     O    opls_236   -0.500     6
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB2
    CB   HB3
    CB    CG
    CG   HG2
    CG   HG3
    CG    SD
    SD    CE
    CE   HE1
    CE   HE2
    CE   HE3
     C     O
    -C     N
 [ dihedrals ] ; override some with residue-specific ones
     N    CA    CB    CG    dih_MET_chi1_N_C_C_C
    CG    CB    CA     C    dih_MET_chi1_C_C_C_CO
  [ impropers ]
    -C    CA     N     H    improper_Z_N_X_Y 
    CA    +N     C     O    improper_O_C_X_Y

I get this error:

Atom HB1 not found in rtp database in residue MET, it looks a bit like HB2

bjwiley23 · July 15, 2022, 8:54am

Basically we need a way for this .hdb entry to start numbering at 2 instead of 1 to comply with PDB naming convention for hydrogens

MET     5       
...
...
2	6	HB	CB	CG	CA
2	6	HG	CG	SD	CB
...

Ugh this is really getting annoying. There should be another column to indicate which number to start numbering with.

See here [gmx-users] how to rename my hydrogens before pdb2gmx
and here http://ligand-expo.rcsb.org/reports/M/MET/atom-names.html

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