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

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 26 01:18:57 CEST 2010 


shahid nayeem wrote:
> HI
> I am using Cytochrome-C  pdb 1hrc.pdb. In pdb2gmx it does not gives
> any eror using ffG43a1. .top file produced shows all bonds (Fe & SD of
> MET 80 and Fe & NE2 of HIS 18) using spec.dat file but all the error
> lines does not have bond/angle nomenclature such as
>   809   810     2    gb_30
>   810   811     2    gb_29
>   810  1068     2
>   812   813     2    gb_4
>   812   814     2    gb_9
>   814   815     2    gb_2
> 810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp
> file of force-field and adding these bonds and giving some name to it
> but got the same error in grompp.

Modifying an .rtp entry will do nothing since this bond exists between two 
(presumably) non-sequential residues.

> Though .top file shows these bonds the .gro file generated does not
> show these bonds in VMD while original pdb file shows these bonds.
> thanking you.

VMD's concept of bonds is irrelevant, it's simply guessing where they should be 
based on interatomic distances.

Unfortunately, GROMACS does not work "out of the box" with heme-containing 
species, but these types of simulations are in no way novel, so obviously 
parameters for these missing terms should be available somewhere.  Consult the 
literature, and if necessary, contact the authors of relevant papers - they 
should be able to reproduce their work, at least, we hope :)

-Justin

> waiting for your suggestion.
> shahid Nayeem
> 
> 
> On 7/15/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> shahid nayeem wrote:
>>> 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.
>> One of the most important choices when conducting MD simulations is the
>> force
>> field.  You'll have to find one that works.  It appears that (unfortunately)
>> the
>> Gromos force fields do not work out of the box when heme is involved.
>>
>> If you want specific advice about other force fields, you'll have to
>> describe
>> your problem much better than "gives error at some point."  No one can help
>> you
>> sort that out.  You'd do well to look into the literature.  Simulations of
>> heme
>> proteins are not novel, so clearly others have made this work, and in some
>> cases, parameters might be provided for the terms that are missing.
>>
>> -Justin
>>
>>> 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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 

-- 
========================================

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

========================================

More information about the gromacs.org_gmx-users mailing list