Hi Mark,

thank you for your answer. It works. I used genrestr for generating the position restrains. I now manually edited the respective lines. Gromacs wants only the parameters for the B state (If you repeat the function type you get an error).


Eg:

123    1    1000   1000   1000   1000   1000   1000

All the best and thanks again

Johannes


On 09.08.2017 11:48, Mark Abraham wrote:
Hi,

I presume the position-restraints file was written by a tool that didn't
anticipate this use case (and pdb2gmx likely does not). If so, I would edit
my position restraints file to express my intent, ie copy the functype and
parameters so that there's an A and B state on the same line, just as with
other topology pieces.

One could also use grompp -maxwarn, but laziness leads to hate, and hate
leads to the Dark Side. You will one day curse Past Hermann, because a
warning you ignored costs you months of wasted simulation time.

Mark

On Wed, Aug 9, 2017 at 11:27 AM Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

Dear all,

I have a questions concerning MD free energy calculations using
alchemical tranformation. I want to restrain the backbone of my protein
which I mutate during TI. However, I do not know how to correctly
generate position restrains. If I use the position restrain file, which
I generated for the A state, following warning shows up:

WARNING 1 [file posre.itp, line 1470]:
    Some parameters for bonded interaction involving perturbed atoms are
    specified explicitly in state A, but not B - copying A to B

Can I ignore this warning, or do you have any suggestions for me?

All the best and thank you very much in advance

Johannes
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