GROMACS version:2021.2
GROMACS modification: Yes
**Here post your question **
Hi, all
I’m trying to simulate protein complex with TPO and SEP in Amber99SB-ildn.ff.
After I edited ‘aminoacids.rtp’, ‘aminoacids.hdb’ and ‘residuestypes.dat’, I simulated my system.
It worked but Gromacs showed some note like:
NOTE 2 [file topol.top, line 27018]:
** In moleculetype ‘Protein_chain_A’ 12 atoms are not bound by a potential**
** or constraint to any other atom in the same moleculetype. Although**
** technically this might not cause issues in a simulation, this often means**
** that the user forgot to add a bond/potential/constraint or put multiple**
** molecules in the same moleculetype definition by mistake. Run with -v to**
** get information for each atom.**
---------------------------------------------------------------------------------------------------------------
I want to solve this problem.
I have followed the instructions on https://manual.gromacs.org/current/how-to/topology.html and used this for SEP and the another for TPO. (I also read another post: https://gromacs.bioexcel.eu/t/adding-sep-parameter-to-amber99sb-ff/2008/5)
I added SEP and TPO to aminoacids.rtp of Amber99SB-ildn as follows:
[ TPO ] ; Phosphothreonine from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
[ atoms ] ; !entry.THP.unit.atoms table
N N -0.493700 1
H H 0.301800 2
CA CT -0.1740 3
HA H1 0.016400 4
CB CT 0.15310 5
HB H1 -0.090900 6
CG2 CT -0.16170 7
HG21 HC 0.049600 8
HG22 HC 0.049600 9
HG23 HC 0.049600 10
OG1 OS -0.637500 11
P P 1.400 12
O1P O2 -0.850 13
O2P O2 -0.850 14
O3P O2 -0.850 15
C C 0.673100 16
O O -0.585400 17
[ bonds ] ; !entry.THP.unit.connectivity table
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB OG1
CG2 HG21
CG2 HG22
CG2 HG23
OG1 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
[ 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
---------------------------------------------------------------------------------------------------------------------------**
Then I added as follow to to aminoacids.hdb.
TPO 4
1 1 H N -C CA
1 5 HA CA N CB C
1 5 HB CB CA CG2 OG1
3 4 HG2 CG2 CB CA
SEP 3
1 1 H N -C CA
1 5 HA CA N CB C
2 6 HB CB CA OG
-----------------------------------------------------------------------------**
Then I added ‘TPO’ & ‘SEP’ as protein in ‘residuestypes.dat’
Just then, I simulated my protein system with Gromacs. And it read as follows:
NOTE 2 [file topol.top, line 27018]:
** In moleculetype ‘Protein_chain_A’ 12 atoms are not bound by a potential**
** or constraint to any other atom in the same moleculetype. Although**
** technically this might not cause issues in a simulation, this often means**
** that the user forgot to add a bond/potential/constraint or put multiple**
** molecules in the same moleculetype definition by mistake. Run with -v to**
** get information for each atom.**
---------------------------------------------------------------------------------------------------------------
I checked ‘atomtypes.atp’, ‘ffnonbonded.itp’ and ‘ffbonded.itp’
After then, I found ‘PS’, ‘O1P’, ‘O2P’ & ‘O3P’ are missing in ‘ffbonded.itp’
I have no idea to add those information in ‘ffbonded.itp’
In my PDB files. The TPO & SEP are as follows:
ATOM 923 N TPO B 95 37.851 2.395 3.475 1.00 15.00 B N
ATOM 924 CA TPO B 95 38.916 2.447 2.489 1.00 15.00 B C
ATOM 925 C TPO B 95 38.989 3.851 1.895 1.00 15.00 B C
ATOM 926 O TPO B 95 40.038 4.285 1.411 1.00 15.00 B O
ATOM 927 CB TPO B 95 38.622 1.445 1.354 1.00 15.00 B C
ATOM 928 CG2 TPO B 95 39.826 1.248 0.444 1.00 15.00 B C
ATOM 929 OG1 TPO B 95 38.179 0.182 1.903 1.00 15.00 B O
ATOM 930 P TPO B 95 39.121 -0.714 2.857 1.00 15.00 B P
ATOM 931 O1P TPO B 95 40.513 -0.239 2.983 1.00 15.00 B O
ATOM 932 O2P TPO B 95 38.501 -1.064 4.147 1.00 15.00 B O
ATOM 933 O3P TPO B 95 39.252 -2.116 2.094 1.00 15.00 B O
ATOM 934 HN TPO B 95 36.988 2.019 3.216 1.00 15.00 B H
ATOM 1087 N SEP B 111 16.135 7.740 1.455 1.00 15.00 B N
ATOM 1088 CA SEP B 111 15.621 8.140 2.758 1.00 15.00 B C
ATOM 1089 C SEP B 111 14.457 9.115 2.596 1.00 15.00 B C
ATOM 1090 O SEP B 111 13.396 8.943 3.207 1.00 15.00 B O
ATOM 1091 CB SEP B 111 16.736 8.767 3.604 1.00 15.00 B C
ATOM 1092 OG SEP B 111 16.588 8.430 4.973 1.00 15.00 B O
ATOM 1093 P SEP B 111 16.287 9.566 6.052 1.00 15.00 B P
ATOM 1094 O1P SEP B 111 15.419 9.126 7.159 1.00 15.00 B O
ATOM 1095 O2P SEP B 111 15.905 10.869 5.479 1.00 15.00 B O
ATOM 1096 O3P SEP B 111 17.698 9.836 6.748 1.00 15.00 B O
ATOM 1097 HN SEP B 111 17.074 7.932 1.236 1.00 15.00 B H
Any advice would be greatly appreciated.
Thanks in advance.
Regards,
Suhyeok.
** I edited the information above as jalemkul said and it worked well!