[gmx-users] PROBLEM REGARDING pdb2gmx & restraints

gurpreet singh gps.iitm at gmail.com
Thu Jun 28 12:21:47 CEST 2007

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

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 ?


Gurpreet singh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070628/868cc7fc/attachment.html>

More information about the gromacs.org_gmx-users mailing list