hello gromacs users<br>
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. <br>
<br>
is it the usual behaviour of gromacs or there is some other mistake in giving the command ?<br>
<br>
pdb2gmx -ff G43a1 -ignh -posrefc 50 -f input.pdb -p toplo.top -o output.pdb -i posre.itp -water spce <br>
<br>
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,<br>
i am little bi doubltful about the way we use these files for maintaing the restraints <br>
<br>
i used in the following way <br>
<br>
grompp -f input.mdp -c somefile.pdb -p toplo.top -r posre_A.itp,posre_B.itp -o output.tpr<br>
<br>
is this the right way to mention the restaints or not ?<br>
<br>
and if i want to change the restraints gradually after each step of the simulation then what is the procedure to do that ?<br>
<br>
THANKS<br>
<br>
Gurpreet singh <br>
IIT MADRAS <br>
<br>
<br>