Thanks Jason for your comments and for taking the time to answer me
In fact there is a stupid mistake on my part about the CMAP values. They are indeed the same between AMBER and GROMACS.
Regarding the dimensions of the simulation box in the *.gro file, they are in indeed nanometres and not in Angstoms. This effectively gives a huge box. In the case of the values of the box given by ParmEd (32x31x33 A) they seem small to me knowing that the inpcrd file contains a big membrane protein surrounded by detergents which cannot fit in a box of this size. In both cases it is not a problem since I always resize the dimensions of the box before adding the solvent
Finally regarding the warning message of ParmEd about 1-4 scaling thank you for the additional information It is very useful for me and all the usets of acepype and GROMACS
Best
Stéphane
----------------------------------------------------------
De : Jason Swails [jason.swails.gmail.com]
Envoyé : lundi 22 novembre 2021 14:52
À : ABEL Stephane
Cc : AMBER Mailing List; alanwilter.gmail.com
Objet : Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? --update
On Thu, Nov 18, 2021 at 7:23 AM ABEL Stephane <Stephane.ABEL.cea.fr<mailto:Stephane.ABEL.cea.fr>> wrote:
Dear all,
Below a little update of of my testing of AMBER19SB with GROMACS(2021.3). I have converted prmto/impcrd files (equivalent to prm7 and rst7) of a protein modeled with the AMBER19SB into GROMACS gro/top files using Parmed (AT21, fully patched) and ACEPYPE (last version).
The AMBER files were obtained using tleap (AT21). From the results below with the same gro file
I used the ParmEd commands below from Jason Swails
import parmed as pmd
parm = pmd.load_file("MYTOPFF19SBparm7", "MYTOPFF19SB.rst7")
parm.save("MYTOPFF19SB.top") # .top saves to GROMACS topology file format
parm.save("MYTOPFF19SB.gro")
```
And execute it as `python <file.py>`. Does that work for you?
The results with the same mdp of GROMACS at step0
>From Parmed (Parmed_Conversion_GROMACS_AMBER19SB.py, VERSION 3.4.1) at step0
Step Time
0 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. CMAP Dih.
1.52227e+03 7.26001e+03 1.15737e+04 2.23252e+02 3.32921e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
1.02351e+04 9.98003e+04 -1.76602e+04 -1.87376e+05 -7.10925e+04
Pressure (bar)
1.77444e-01
[snip]
>From Sander with coordinates file but not the same
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -15720.7550 EKtot = 0.0000 EPtot = -15720.7550
BOND = 348.4593 ANGLE = 1731.7886 DIHED = 2819.0630
1-4 NB = 2449.9439 1-4 EEL = 23852.5075 VDWAALS = -4733.5065
EELEC = -42775.8491 EHBOND = 0.0000 RESTRAINT = 0.0000
CMAP = 586.8384
SANDER* (AT21) Kcal/mol** (KJ/mol)*** with 1kjoul/mol = 4.1867 Kcal/mol
**
step 0
BOND = 348.4593* = 1458.89** ---> Similar to GROMACS results above
ANGLE = 1731.7886 = 7250.479** ---> Similar to GROMACS results above
DIHED = 2819.0630 = 11802.57** Similar to GROMACS results above (Proper Dih + Improper Dih)
CMAP = 586.8384 = 3.32921e+03 ---> Different from GROMACS obtained with ParmEd (3.32921e+03)
Am I missing something? The CMAP terms look identical?
* | mdin Single point
; see
http://ringo.ams.stonybrook.edu/index.php/2012_AMBER_Tutorial_with_Biotin_and_Streptavidin
&cntrl<
http://ringo.ams.stonybrook.edu/index.php/2012_AMBER_Tutorial_with_Biotin_and_Streptavidin&cntrl>
imin=0,
ntpr=1,
maxcyc=100,
ntmin=2,
ntb=0,
igb=0,
cut=999
/
on can say
1) The converted file generated by ParmEd is well recognized by GROMACS and in particular the CMAP term. IT is not the case from the file obtained bt ACEPYPE (since it does not support CMAP for AMBER yet)
2) CMAP energy in AMBER and GROMACS are different
Unless I'm misreading your email, the CMAP energies between AMBER and GROMACS look the same.
2) the calculations of the energy for the other bonded and non bonded are the same (with rounding error)
2) WARNING !!! with the same inpcrd Parmed does not genertae a corrct GRO file. The box is to too small
3.24900 3.12110 3.31620 ---> end gro file from ParmEd
117.23400 182.43200 135.66400 ---> end gro file from ACEPYPE
For box dimensions, the acpype numbers you post look absurd -- that's a 1172x1824x1356 angstrom box (compared to the more reasonable 32x31x33 angstrom box that is more prototypical of what tleap will generate when solvating a system).
3) Note that at this moment ParmEd seems not support mixing 1-4 LJ if the prmtop contains atom types from GRLYCAM06 and AMBER19SB ffields. The program crashes with the following error
Traceback (most recent call last):
File "Parmed_Conversion_GROMACS_AMBER19SB.py", line 3, in <module>
parm.save("ShuA_BOG_AMBER19SB_GLYCAM06_HMASS_From_Parmed.top") # .top saves to GROMACS topology file format
File "/home/stephane_abel/amber20/lib/python3.9/site-packages/parmed/structure.py", line 1489, in save
s = gromacs.GromacsTopologyFile.from_structure(self)
File "/home/stephane_abel/amber20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 1279, in from_structure
raise GromacsError('Structure has mixed 1-4 scaling which is '
parmed.exceptions.GromacsError: Structure has mixed 1-4 scaling which is not supported by Gromacs
This is not a ParmEd limitation - it's a GROMACS one. GROMACS doesn't let you specify pair-specific 1-4 electrostatic terms (it does for Lennard-Jones, but not electrostatic). As a result, it's fundamentally impossible to represent a mixed-scaling system with a GROMACS topology file. Rather than generate something that is "close" (but still wrong in definition), ParmEd throws an error. I would urge strong caution if acpype generates a GROMACS topology file from a mixed force field like this, as the 1-4 terms are unlikely to match exactly.
If the sugar or non-sugar components to the system are small, then the difference in 1-4 electrostatic contributions may be small enough to escape detection (i.e., be confused with round-off/precision errors), but in this case the treatment is actually wrong (which would be easier to observe by looking at the computed forces, most likely).
All the best,
Jason
--
Jason M. Swails
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Received on Mon Nov 22 2021 - 09:00:02 PST
