hello gromacs users my question is regarding the command pdb2gmx which is the first step to process ur input file. i used the force field 43a1 and i m doing some dimeric protein simulation . when i checked the output of the pdb2gmx command i found that this command have not added any hydrogens to the carbon atoms of the protein although to other heavy atoms hydrogens were added.
is it the usual behaviour of gromacs or there is some other mistake in giving the command ? pdb2gmx -ff G43a1 -ignh -posrefc 50 -f input.pdb -p toplo.top -o output.pdb-i posre.itp -water spce my second question is about the positional restraints. since i have the dimer so after using the pdb2gmx i got the two posre_A.itp & posre_B.itp files for putting the restriants, i am little bi doubltful about the way we use these files for maintaing the restraints i used in the following way grompp -f input.mdp -c somefile.pdb -p toplo.top -r posre_A.itp,posre_B.itp -o output.tpr is this the right way to mention the restaints or not ? and if i want to change the restraints gradually after each step of the simulation then what is the procedure to do that ? THANKS Gurpreet singh IIT MADRAS
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