Hello,
I am trying to run FEP on a molecule to convert it from a protonated to an unprotonated form. When running grompp, I initially got the error:
ERROR 1 [file pap2.itp, line 140]:
Proper Dih. multiplicity can not be perturbed 2.000000!=4.000000
I went and explicitly added the B state dihedrals next to the A state dihedrals on line 140 but this didn’t fix it. How can I correctly fix the .itp file?
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c0_B c1_B c2_B c3_B
3 4 7 8 9 ; CG2R61 CG2R61 CG321 CG2O2 CG2R61 CG2R61 CG321 CG2O3
I also tried adding it below but that didn’t work either.
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
3 4 7 8 9 ; CG2R61 CG2R61 CG321 CG2O2
3 4 7 8 9 ; CG2R61 CG2R61 CG321 CG2O3
The error message it quite clear: you can not change the multiplicity of a dihedral.
The solution here is to change the parameters of the dihedral type with multiplicity 2 to use multiplicity 4 and a zero parameters for the higher order terms. This gives the same potential, but now with the multiplicity set to 4.
Ok. I played around and set c2 and c3 to 0.0 on line 140:
3 4 0.0 0.0 9 ; CG2R61 CG2R61 CG321 CG2O2
After doing so, I get the following warning:
WARNING 3 [file pap2.itp, line 140]:
Too few parameters on line (source file
/tmp/gromacs-20220116-70506-1iya1kj/gromacs-2021.5/src/gromacs/gmxpreprocess/toppush.cpp, line 1908)
Also, I am now getting these errors past line 151:
ERROR 1 [file pap2.itp, line 151]:
Cannot automatically perturb a torsion with multiple terms to different
form.
Please specify perturbed parameters manually for this torsion in your
topology!
I am guessing, but could it be how I set the state B of the Hydrogen atom to a dummy atom?
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
18 HGP1 1 PAP H8 18 0.430 1.008 DUM 0 1e-6
I understand what’s going on now. I first need the explicit dihedrals. Could you point me to how I can get these values? CGenFF did not calculate those for me when I used it.