[gmx-users] Protein_ligand simulation

RAHUL SURESH drrahulsuresh at gmail.com
Sat Jul 28 15:22:11 CEST 2018

Hi all

I am performing a simulation between a protein and Fluorine molecule. I
have optimized the F2 structure using Gaussian and inserted into the box
using gmx insert-molecules command after adding solvent [gmx solvate]. The
topology for fluorine molecule is generated by topolgen.

*[ moleculetype ]; Name            nrexclFLU1                3[ atoms ];
nr       type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB      massB     1   opls_164      1   FLU1      F      0
-0.206   18.99840                                  2   opls_164      1
FLU1      F      0     -0.206   18.99840                             [
bonds ];  ai    aj funct    1     2     1    ;     F     F[ pairs ];  ai
aj funct[ angles ];  ai    aj    ak funct[ dihedrals ];  ai    aj    ak
al funct*

On command  gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr i get
the following errors

*ERROR 1 [file fluorine.itp, line 21]:  No default Bond types*

*NOTE 1 [file alz.top, line 5915]:  System has non-zero total charge:
-23.600000  Total charge should normally be an integer. See
<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>  for
discussion on how close it should be to an integer.*

*WARNING 1 [file alz.top, line 5915]:  16639 non-matching atom names  atom
names from alz.top will be used  atom names from alz_F.gro will be ignored*

Indeed there are only 628 atoms in .top file.

Any suggestions?

*Rahul *

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