[gmx-users] Grompp error: No default g96angle type

[shahid nayeem]

Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined  in this file.
 Using other options of force field also gives error at some point.
waiting for your suggestion to proceed further.
shahid Nayeem

On 7/15/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> shahid nayeem wrote:
>> Dear All
>> I used the following command sequentially to prepare file for energy
>> minimization and subsequent MD run.
>> 1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
>> 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
>> 3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
>> 4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
>> grompp gives following error.processing topology...
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
>> Generated 279 of the 1225 non-bonded parameter combinations
>>
>> ERROR 1 [file seq.top, line 1965]:
>>   No default G96Bond types
>>
>>
>> ERROR 2 [file seq.top, line 5271]:
>>   No default G96Angle types
>>
>>
>> ERROR 3 [file seq.top, line 5272]:
>>   No default G96Angle types
>>
>>
>> ERROR 4 [file seq.top, line 5648]:
>>   No default G96Angle types
>>
>>
>> ERROR 5 [file seq.top, line 5653]:
>>   No default G96Angle types
>>
>>
>> ERROR 6 [file seq.top, line 5654]:
>>   No default G96Angle types
>>
>>
>> ERROR 7 [file seq.top, line 5655]:
>>   No default G96Angle types
>>
>>
>> ERROR 8 [file seq.top, line 5656]:
>>   No default G96Angle types
>>
>>
>> ERROR 9 [file seq.top, line 6201]:
>>   No default Proper Dih. types
>>
>> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
>> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
>> Excluding 3 bonded neighbours molecule type 'Protein_A'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>>
>> NOTE 1 [file seq.top, line 6932]:
>>   System has non-zero total charge: 7.000001e+00
>>
>>
>>
>> processing coordinates...
>> double-checking input for internal consistency...
>> renumbering atomtypes...
>> converting bonded parameters...
>>
>> There was 1 note
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.7
>> Source code file: grompp.c, line: 986
>>
>> Fatal error:
>> There were 9 errors in input file(s)
>> -------------------------------------------------------
>>   pdb2gmx works properly using ff43a1 forcefield. My protein contains
>> Heme. I was having N-terminal ACE group which I simply deleted from
>> the pdb.
>> Am I right in deleting this group. How should I proceed to get rid of
>> this error.
>>
>
> That seems like a particularly poor solution.  Simply getting rid of an
> inconvenient group does not sound appropriate.  Ask yourself whether or not
> there is some functionally significant reason to having the ACE group there
> (chain truncation? artificial modification?) and decide.
>
> As for the errors, look into the topology to see which atoms are causing the
> problems.  Then decide if there are indeed appropriate parameters in the
> force
> field for this task.
>
> -Justin
>
>> Thanks in anticipation of help.
>> Shahid Nayeem
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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