[gmx-users] Strange error message when trying to preprocess a cyclotide in GROMACS

Matthew Stancea mstancea at ggc.edu
Thu Jun 26 22:28:28 CEST 2014

Hello again!

Because of the help of Dr. Lemkul and Dr. Abraham, I was able to successfully generate a gromacs topology of a cyclotide from a pdb file!

(The command I used was "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter".)

In the generated file, the only issue was that there were a total of three hydrogens bonded to the beginning nitrogen and a total of two oxygens bonded to the ending carbon. Since all of the other information was correct, I did these steps in this order so that I could generate a completely correct cyclotide gromacs topology:

First, I visualized the structure using vmd and took note of which two of the three hydrogens needed to be removed and which oxygen of the two needed to be removed.

Second, I edited the conf.gro file and the topol.top file, and I removed the three lines correspondin to the extraneous atoms.

Third, I used a python script to rename the conf.gro atom numbers.

Fourth, I used another python script to simultaneously rename the atom numbers for the section "[ atoms ]", create an index for the previous number and the new number, and use that index to renumber the sections "[ bonds ]", "[ pairs ]", "[ angles ]", and "[ dihedrals ]". (I had no entries for the second section of dihedrals.)

Lastly, after attempting to preprocess, I discovered some of the entries in "[ bonds ]" and  "[ angles ]" were renumbered twice (therefore containing erroneous connections), and so I manually renumbered them to reference the correct atoms.

After this process, I once again attempted to preprocess, but this time I received the following message:

NOTE 1 [file grompp.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Setting the LD random seed to 17692
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations

ERROR 1 [file topol.top, line 1839]:
  No default Angle types

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...

NOTE 2 [file topol.top, line 3598]:
  System has non-zero total charge: 0.454300
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

Warning: atom name 2 in topol.top and conf.gro does not match (H1 - H)

WARNING 1 [file topol.top, line 3598]:
  1 non-matching atom name
  atom names from topol.top will be used
  atom names from conf.gro will be ignored

There were 2 notes

There was 1 warning

Program grompp_mpi, VERSION 4.6.2
Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/grompp.c, line: 1593

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

?Any help would be most appreciated!

Matthew Stancea

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