Dear Amber experts,
I wanted to use Panteva parameters for my simulations, so I followed this
tutorial: https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
However, with the tleap_1264_tip4pew.in
<
https://ambermd.org/tutorials/advanced/tutorial20/files/1264/tleap_1264_tip4pew.in>
file being unavailable, I'm not sure if I follow correctly.
Below is my version of how the file should look like:
source leaprc.DNA.OL15
source leaprc.water.tip4pew
loadamberparams frcmod.ions234lm_126_tip4pew
mol = loadpdb 1D23_clean.pdb
solvatebox mol TIP4PEWBOX 10.0
loadamberparams frcmod.tip4pew
addions mol MG 0
check mol
savepdb mol 1D23_solv.pdb
saveamberparm mol 1D23_solv.prmtop 1D23_solv.inpcrd
quit
tLeaP does not report any errors (just some warnings about water atoms
being close to each other). Then I use parmed according to the tutorial,
and I got the following error after the last command, so when trying to
save the modified prmtop and incprd files:
Traceback (most recent call last):
File "/u/k/kmitusin/miniconda3/envs/AmberTools23/bin/parmed", line 11, in
<module>
sys.exit(clapp())
^^^^^^^
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/scripts.py",
line 142, in clapp
parmed_commands.cmdloop()
File "/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/cmd.py",
line 138, in cmdloop
stop = self.onecmd(line)
^^^^^^^^^^^^^^^^^
File "/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/cmd.py",
line 217, in onecmd
return func(arg)
^^^^^^^^^
File "<string>", line 1, in <lambda>
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/tools/parmed_cmd.py",
line 158, in _normaldo
action.execute()
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/tools/actions.py",
line 274, in execute
self.parm.save(self.rst_name, format=self.rst7_format,
overwrite=Action.overwrite)
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/structure.py",
line 1578, in save
rst7.write(fname, netcdf=(format == 'NCRST'))
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/amber/_amberparm.py",
line 2360, in write
f.coordinates = self.coordinates
^^^^^^^^^^^^^
File
"/u/k/kmitusin/miniconda3/envs/AmberTools23/lib/python3.12/site-packages/parmed/amber/asciicrd.py",
line 322, in coordinates
raise ValueError(f'Got {len(stuff)} coordinates for {self.natom} atoms')
ValueError: Got 1 coordinates for 15885 atoms
As you can see I'm using Amber22 AmberTools23, conda version.
So my first question is: why do I obtain this error? Is there something
wrong with how I prepare the prmtop and inpcrd files?
The second question is regarding the A and B coefficients: as the values
I'm getting are almost a half of the value shown in the tutorial. How are
they determined? And of course - why are mine different?
For example:
mine:
Atom Type 1 Atom Type 2 A coefficient B coefficient C
coefficient R i,j Eps i,j
Mg2+ [16] NAMG [19] 42306.775035 82.288023
238.750000 3.177000 0.040013
Mg2+ [16] NGMG [20] 42306.775035 82.288023
240.625000 3.177000 0.040013
Mg2+ [16] OPMG [21] 25012.281982 66.703853
21.250000 3.014200 0.044472
tutorial:
Mg2+ [16] NAMG [19] 88850.011883 148.040958
238.750000 3.177000 0.040013
Mg2+ [16] NGMG [20] 88850.011883 148.040958
240.625000 3.177000 0.040013
Mg2+ [16] OPMG [21] 53402.610012 120.997661
21.250000 3.014200 0.044472
Thank you for your help.
Best regards,
Karolina Mitusińska
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Received on Thu Jul 17 2025 - 03:30:02 PDT
