[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Mon Jun 16 18:31:57 CEST 2014

Dr. Justin Lemkul,

>> Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like?

>The final columns specify the new residue names that should be assigned to the
>residues only in the case that a special bond was created.  You'll see from the
>existing Cys specifications that a residue named "CYS" (standard PDB
>nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but
>only if a special bond is created.  The nomenclature exists because of the way
>the force fields work.  In your case, you don't need to rename anything, so
>preserving the original residue names is the proper way to go.

>Of course, the answer to "is this correct?" is generally obtained by running it ;)

>> 3
>> CYS     N       1       VAL     C       1       0.132    CYS    VAL
>> CYS     SG      1       CYS     SG      1       0.20    CYS2    CYS2
>> CYM     SG      1       CYM     SG      1       0.20    CYS2    CYS2

With the above specbond.dat file in the working directory, I attempted the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp" and received this fatal error message (it is the same as the original):

Program pdb2gmx_mpi, VERSION 4.6.2
Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727

Fatal error:
Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-Matthew Stancea

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