Dear sir,
i'm a new user of gromacs.i've done the installation correctly.while
simulating my protein i encounter some of the problems.please give me ur
suggetions or any reference to overcome this problem.this is my first
experience of running the gromacs.kindly look for my problems and answer
me
as soon as possible.Thanks in advance........some of the errors are..
1..while running pdb2gmx
warning :'FE2' not found in residue topology database,trying to use
'FE'.i know that i've to use PRODGR to construct topology for Fe.but i'm
not
familiar to use it.please tell me the procedure of using it.
2..when i'm trying to run grompp
Note: System has non-zero total charge : -6.000002e+00.is it
necessary
to neutralise the charge, if so genion has to run Na means how much i've
to
add..ie how to calculate it...
3..with the avialable output file i tried to run mdrun..
showing the error that can not open File toplo.tpr but my tpr file is
out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o out4
-c
out4 -v..........plz give me ur advice to overcome.
i'll be helpful if i get the answers..
thanking you,
lali
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