minal option %s:%s for residue
%s"%(v,k,resname))
if not found: print("Unknown option but trying anyway:",selectedOption)
p.sendline(selectedOption)
except pexpect.EOF:
print(p.before)
except pexpect.TIMEOUT:
print("TIMEOUT"
Hi,
The name of the residue in that force fields aminoacids.rtp is CLA, which
is the only thing pdb2gmx can understand. Otherwise your procedure should
just work if you rename your ion residues appropriately. Do let us know how
you go!
Mark
On Wed, Jul 18, 2018, 03:23 Anderson, Amos wrote:
>
On 7/17/18 9:22 PM, Anderson, Amos wrote:
Hi Gromacs users,
I’ve never used gromacs before, so sorry if this question has an obvious answer
somewhere — it seems like the sort I should have been able to find an answer
for…
I want to write a python script to prepare an arbitrary pdb for use
Hi Gromacs users,
I’ve never used gromacs before, so sorry if this question has an obvious answer
somewhere — it seems like the sort I should have been able to find an answer
for…
I want to write a python script to prepare an arbitrary pdb for use with
gromacs (e.g., does these steps
