[gmx-users] special bond

[Nicola Staffolani]

​​Hi Justin,

thank you very much for caring!

​
On Tue, Apr 29, 2014 at 6:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> It would be helpful to see:
>
1. The actual error messages.
> 2. The lines of the topology to which they correspond.
> ​
>

​
*ERROR 1 [file speptide.top, line 3224]:  No default G96Bond types*
​​

​
line 3224 of speptide.top:  *1239  1264     2 *

...
*​*



*​ERROR 911 [file speptide.top, line 12119]:  No default G96Angle types​*
line 12119 of speptide.top:*  1412  1437  1462     2 *

...



*​ERROR 3590 [file speptide.top, line 15794]:  No default Proper Dih. types*

​line 15794 of speptide.top:  *1762  1787  1788  1763     1 *​

​As ​you can see, it looks like the errors are generated because no gb, no
ga and no gd are there... The gb's are looked for because I have told
gromacs in *specbond.dat* to put* special bonds *between *those* couple of
atoms - I mean, the couple of atoms it tries to (special) bond are exactly
those I have requested to...

The thing you should know is that the Gromos force fields work in a manner
> that is different from basically all the others in Gromacs.  The fact that
> "gb_99" doesn't show up in the .top file is actually not really a problem -
> the parameters will be looked up from [bondtypes].  The explicit use of
> gb_*, ga_*, etc. is merely a convenience.  One can always override whatever
> is listed in [bondtypes] by writing in their own parameters in the .top
> file.  Is grompp complaining about missing parameters (i.e. "no default
> bondtypes") for your special bond?
>

​I guess I have answered this question with my previous lines, so the
answer is yes, grompp is complaining ... ​

-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36