[gmx-users] Re: warning mesgs

[rams rams]

HI,

When I use the merge command along with pdb2gmx to form inter disulphide
bonds between two different chains, its removing a water molecule to connect
the two ends. Its like forming a peptide bond which I dont wish. Is there
any way to tell to gromacs, to create the inter dishulphide bonds without
creating the peptide bond between the two chains ?



On Fri, Jun 27, 2008 at 6:51 PM, rams rams <rams.crux at gmail.com> 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
> ??
>
> Ram.
>
>
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