Dear all,
I am trying to calculate the number of water molecules at a distance of 0.35A from the protein. I used two gmx select GROMACS codes which have given me different answers.
1. gmx_mpi select -s em.tpr -f md_Pro1.xtc -os Pro1_prowater1.xvg -n index.ndx -select "res_com of resname SOL and within 0.35 of group Proteinwhole" (no. of molecules - 247)
2. gmx_mpi select -s em.tpr -f md_Pro1.xtc -os Pro1_prowater2.xvg -n index.ndx -select 'name OW and within 0.35 of group "Proteinwhole"' -selrpos atom -seltype res_com -on no.water.ndx (no.of molecules - 208)
I have looked into previous threads which have dealt with similar questions but those discussions did not clarify my doubt. Seeking help to find the best method to get the correct number of water molecules.
There are many ways but it is hard to say which one is the best. The only thing you need to do in determining the number of water molecules is calculating the distance between the protein and each water molecule, and grabbing the atom number or residue number, which could be done with many trajectory tools. For instance, the distance tool in gromacs could do this. Some patches such as PLUMED can also give you this information. Some python lib such as mdtraj and trajectory tools in other software such as cpptraj in AMBER could also be used to perform this distance calculation.
You should just try one and build your own workflow/script for this calculation.
Thanks @ Zhaoxi Sun for your reply. I agree that there are a many ways to arrive at the number of water molecules. However, I am just curious about the different answers obtained with the same gmx select options. With option 1, I guess I am selecting the water molecule named as "SOL" and with option 2, I have selected the oxygen atoms of the water molecules. Both options should ideally give the same answer. Wondering what difference does the selection terms make?
Hi
You can try the following command line:
gmx select -f -s -n -of -ofpdb -selrpos atom -seltype res_com -select 'group X and within 0.4 of group Y'
X =group with protein atoms
Y =group with water atoms
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