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Hello All,
I am having a lot of issues to simulate a phosphoserine on the GROMACS and I have no idea how to fix it since I am pretty new to MD with GROMACS. This is what I have done to add the phosphoserine from previous posts, but it is still not working for me. I have this error pop up but I am not sure how to fix it.
Fatal error:
Residue 3 named SEP of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
This is what I have done:
Adding SEP aminoacids.rtp:
[ SEP ] ; Phosphoserine from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
[ atoms ] ; !entry.SEP.unit.atoms table
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 ] ; !entry.THP.unit.connectivity table
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG P
P O1P
P O2P
P O3P
C O
-C N ; is present everywhere else
[ impropers ] ; is present everywhere else
-C CA N H
CA +N C O
Adding SEP to aminoacids.hdb:
SEP 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA OG
SEP as protein in ‘residuestypes.dat
After I did all of that, I tried gmx pdb2gmx -f filename.pdb -o filename.gro -p filename.top -ignh. Choose Amber99sb-ildn and none for water.
**Here is my pdb for SEP if it would help. I prepare the unmodified peptides with Chimera and add phosphorylation via CHARMMGUI. Peptide sequence: FQsEEQQQTEDELQDK: **
ATOM 40 N SEP P 3 -6.586 -2.995 -5.211 1.00 0.00 PROA
ATOM 41 HN SEP P 3 -7.332 -3.559 -5.564 1.00 0.00 PROA
ATOM 42 CA SEP P 3 -6.855 -2.396 -3.919 1.00 0.00 PROA
ATOM 43 HA SEP P 3 -6.778 -1.325 -4.054 1.00 0.00 PROA
ATOM 44 CB SEP P 3 -8.200 -2.846 -3.372 1.00 0.00 PROA
ATOM 45 HB1 SEP P 3 -8.992 -2.505 -4.077 1.00 0.00 PROA
ATOM 46 HB2 SEP P 3 -8.251 -3.958 -3.335 1.00 0.00 PROA
ATOM 47 OG SEP P 3 -8.413 -2.253 -2.088 1.00 0.00 PROA
ATOM 48 P SEP P 3 -9.759 -2.558 -1.279 1.00 0.00 PROA
ATOM 49 O1P SEP P 3 -10.943 -2.090 -2.034 1.00 0.00 PROA
ATOM 50 O2P SEP P 3 -9.872 -4.002 -0.973 1.00 0.00 PROA
ATOM 51 O3P SEP P 3 -9.699 -1.767 0.087 1.00 0.00 PROA
ATOM 52 HT SEP P 3 -10.464 -1.880 0.656 1.00 0.00 PROA
ATOM 53 C SEP P 3 -5.782 -2.804 -2.920 1.00 0.00 PROA
ATOM 54 O SEP P 3 -5.251 -1.962 -2.199 1.00 0.00 PROA
Any advice would be greatly appreciated.
Thanks in advance.
Nhat