[gmx-users] warning mesgs

[Justin A. Lemkul]

rams rams wrote:
> Hi,
>
> I have three di sulphide bonds in my crystal structure. In the 
> topology file it left blanks at the corresponding sulphur 
> connectivities (i.e., values corresponding to gb_, ga_. gd_ ). When I 
> try to create the .tpr file it complains the following:
>
> processing topology...
> Generated 716 of the 2628 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1046 of the 2628 1-4 parameter combinations
> WARNING 1 [file "insu_pwi.top", line 607]:
>   No default G96Bond types, using zeroes
> WARNING 2 [file "insu_pwi.top", line 745]:
>   No default G96Bond types, using zeroes
> WARNING 3 [file "insu_pwi.top", line 2008]:
>   No default G96Angle types, using zeroes
> WARNING 4 [file "insu_pwi.top", line 2209]:
>   No default G96Angle types, using zeroes
> WARNING 5 [file "insu_pwi.top", line 2345]:
>   No default G96Angle types, using zeroes
> WARNING 6 [file "insu_pwi.top", line 2512]:
>   No default G96Angle types, using zeroes
> WARNING 7 [file "insu_pwi.top", line 2748]:
>   No default Proper Dih. types, using zeroes
> WARNING 8 [file "insu_pwi.top", line 2820]:
>   No default Proper Dih. types, using zeroes
> WARNING 9 [file "insu_pwi.top", line 2863]:
>   No default Proper Dih. types, using zeroes
> WARNING 10 [file "insu_pwi.top", line 2919]:
>   No default Proper Dih. types, using zeroes
> Cleaning up temporary file gromppID2O6e
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: fatal.c, line: 416
>
> Fatal error:
> Too many warnings, /usr/local2/gromacs/bin/grompp terminated
> -------------------------------------------------------
>
> "Encountered Subspace Anomaly" (Star Trek)
>
> MD_insu.tpr was not created. Check for errors. Exiting ...
>
> Is there a way to fix it ? Also what are those b_, ga_. gd_ 
> corresponds to ??
>

Were there any warning messages from pdb2gmx?  I assume you somehow got 
through the problems we were discussing previously?  How did you do it 
(i.e., what command did you give pdb2gmx)?

gb, ga, and gd correspond to G96Bond, G96Angle, and G96Dihedral 
parameters from the *bon.itp file.  These shouldn't be a problem if the 
disulfides were properly created, so I suspect there is some unresolved 
problem from earlier in your system preparation.

-Justin

> Ram.
>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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