I am using GROMACS 2024.1 and
during the pdb2gmx step, you apply the -ignh flag, which successfully generates the .gro and .top files.
However, I notice that the water molecules in the PDB file are being removed as a result of this process, which is not my intention. I amseeking a solution to prevent the removal of water molecules while still using the -ignh option.
on other hand if I run without -ignh i have errors regarding Fatal error:
Atom HB3 in residue LYS 3 was not found in rtp entry LYS with 22 atoms
while sorting atoms.
So what is the right way to retain these water molecules and process
remove the hydrogen atoms from the protein and let the gmx pdb2gmx assign the hydrogen atoms, or rename the atoms as per the rtp entry in the corresponding force field.
you can use flags to assign charges/protonations states if you want. Regarding the water molecule is confusing? do you have a system with water molecule? and you wanted to pass that through gmx pdb2gmx?
yes, I mean my system contain additional water molecules too in my PDB file. I just want to generate the .gro and .top file and retain those water molecules.
keeping the name convection with the water definition in the force field is removing the hydrogen atoms? can you paste the water molecule part pdb file, which ff and water model you are using?
I am running like this
gmx pdb2gmx -f modified_file.pdb -o processed.gro -water spce -ignh
I am using the
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) forcefield option.
I am running with -ignh to get the .gro and .top file but I want to retain the water molecules present in my pdb
if it is tip3p water in amber represented as OW, HW1 and HW2.
Remove the hydrogen from protein/rename according to Amber94 and process it like
gmx pdb2gmx -f protein.pdb
its spce as mentioned above
check the ff folder and name accordingly.
I did. I removed the Hydrogens in the protein, I had only the Water molecule hydrogens+ aminoacids without hydrogen,
Now when I run without using -ignh option just
gmx pdb2gmx -f modified_file.pdb -o waterrefprocessed.gro -water spce
I still see that all my water molecules are removed in my .gro file except one, I am not understanding why its not retaining those water SOL
HETATM>> ATOM please check the ff files related to water and protein, you need to defined the input pdb as per the definition in the FF files.
Then run
gmx pdb2gmx -f modified_file.pdb
Input.pdb:
REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-04-12
ATOM 1 N ALA A 1 132.640 119.790 118.780 1.00 0.00 N
ATOM 2 CA ALA A 1 133.450 119.900 117.550 1.00 0.00 C
ATOM 3 CB ALA A 1 134.640 120.850 117.800 1.00 0.00 C
ATOM 4 C ALA A 1 133.940 118.530 117.130 1.00 0.00 C
ATOM 5 O ALA A 1 133.470 117.500 117.630 1.00 0.00 O
ATOM 6 N ALA A 2 134.880 118.520 116.190 1.00 0.00 N
ATOM 7 CA ALA A 2 135.430 117.310 115.610 1.00 0.00 C
ATOM 8 CB ALA A 2 135.370 117.410 114.090 1.00 0.00 C
ATOM 9 C ALA A 2 136.840 117.090 116.080 1.00 0.00 C
ATOM 10 O ALA A 2 137.620 118.040 116.070 1.00 0.00 O
HETATM33089 OW SOL A 1 152.030 130.970 99.280 1.00 0.00 O
HETATM33090 HW1 SOL A 1 151.920 131.910 99.610 1.00 0.00 H
HETATM33091 HW2 SOL A 1 151.980 130.340 100.050 1.00 0.00 H
TER 33092 SOL A 1
HETATM33093 OW SOL A 1 153.690 135.340 95.010 1.00 0.00 O
HETATM33094 HW1 SOL A 1 154.300 136.140 95.050 1.00 0.00 H
HETATM33095 HW2 SOL A 1 152.740 135.650 95.080 1.00 0.00 H
TER 33096 SOL A 1
END
Output.gro:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
26
1ALA N 1 13.264 11.979 11.878
1ALA H1 2 13.187 11.917 11.862
1ALA H2 3 13.321 11.943 11.952
1ALA H3 4 13.230 12.069 11.903
1ALA CA 5 13.345 11.990 11.755
1ALA HA 6 13.286 12.026 11.683
1ALA CB 7 13.464 12.085 11.780
1ALA HB1 8 13.519 12.092 11.697
1ALA HB2 9 13.430 12.175 11.805
1ALA HB3 10 13.521 12.049 11.854
1ALA C 11 13.394 11.853 11.713
1ALA O 12 13.347 11.750 11.763
2ALA N 13 13.488 11.852 11.619
2ALA H 14 13.523 11.940 11.586
2ALA CA 15 13.543 11.731 11.561
2ALA HA 16 13.487 11.655 11.594
2ALA CB 17 13.537 11.741 11.409
2ALA HB1 18 13.575 11.658 11.369
2ALA HB2 19 13.442 11.752 11.380
2ALA HB3 20 13.590 11.820 11.379
2ALA C 21 13.684 11.709 11.608
2ALA OC1 22 13.714 11.619 11.639
2ALA OC2 23 13.762 11.804 11.607
0HOH OW 24 15.203 0.000 0.000
0HOH HW1 25 15.192 0.000 0.000
0HOH HW2 26 15.198 0.000 0.000
2.01610 12.17541 11.95204
I tried changing all ways as per spce.itp in
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) forcefield option.
nothing works
Any help please, this is a sample input and output
change all
HETATM >> ATOM,
what is the issue in your protein/peptide? if it is related to terminal residues, check the definitions for corresponding terminals.
Hi scinikhil Thank you, I have changed everything even HETATM >> ATOM but still not able to fix my issue
I changed the residue number in increasing order for the SOL I am able to retain few water moelcules not all and also the coordinates are getting changed and not able to preserve my previous input
share the files, so that i can have a look
