I would like to generate parameters for small molecule using CGenFF. I
generated str file using cgenFF. However, I could not convert to itp file
using cgenff_charmm2gmx.py because of following error:
Please advice me.
NOTE2: Please be sure to use the same version of CGenFF in your simulations
Couple of methods come to mind:
# cut the box into slices, small enough so that angle between the tube
axis and line to the AA has little effect on the distance. Then do
COM to AA analysis in each slice, then "add" the slice results
together. This is an approximation.
# align tube axis along one
Sorry for the double post, I resend my message (below) since I have received no
response from you guys
Hello,
I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated
with gmx_mpi densmap. For example If I use the following xpm
Hi Farial,
Do not run acpype like this using python "python acpype.py -i XXX.pdb -b
XXX -o gmx".
Just type only *acpype -h* in the terminal and check whether it is
installed or not?.
If it is working,
Then write the command like this:
*acpype -i FFF.pdb -b FFF -o gmx*
*No python command before
Dear Bhupendra
I installed anaconda on /home/vaio/ and then issued the same command that
you wrote
conda install -c acpype -c openbabel -c ambermd
but faced with this error:
CondaValueError: too few arguments, must supply command line package specs
or --file
the python version that I have, is
Dear Bhupendra
Thank you for your replying.
I typed the same command that you said: conda install -c acpype -c
openbabel -c ambermd
but the system said :
conda: command not found
or but when I typed : "python acpype.py -i XXX.pdb -b XXX -o gmx" or
"python acpype.py -i XXX.mol2 -o gmx" faced to
