[gmx-users] Simulating conjugated protein

Sanket Ghawali sanket.ghawali at gmail.com
Wed May 25 06:55:08 CEST 2016

Dear, gmx-users,

Hello everyone,

I'm simulating a peptide in an SDS micelle, where my peptide is conjugated
to a organic compound at the N terminal. The SDS micelle was genrated using
CHARMM-GUI, here I am stuck with a problem for adding atom types for the
compound. I tried adding atomtypes for the compound into the .rtp files of
the CHARMM forcefield but when i try to run pdb2gmx it throws an error
regarding missing residues in .hdb file.

I edited the .hdb file adding the hydrogen atom information for the unknown
compound. The pdb2gmx worked this time but it throws back an error while
adding ions.

I tried using SwissParam to parameterized the unknown molecule, using this
i find that the compound does not remain bound to the peptide at the N
terminal even after merging the compound and peptide co ordinates.

The errors which i get while adding ions:

ERROR 190 [file topol.top, line 3284]:
  No default Proper Dih. types

ERROR 191 [file topol.top, line 3285]:
  No default Proper Dih. types

ERROR 192 [file topol.top, line 3286]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'SDS'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 1 [file topol.top, line 3377]:
  System has non-zero total charge: 17.180007
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

Program grompp, VERSION 4.6.5
Source code file: /root/Downloads/gromacs-4.6.5/src/kernel/grompp.c, line: 563

Fatal error:
number of coordinates in coordinate file (sol.gro, 15465)
             does not match topology (topol.top, 15450)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"Being Great is Not So Good" (Red Hot Chili Peppers)


Any suggestions on how to go about doing this?



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