[gmx-users] Re: warning mesgs

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 30 12:45:45 CEST 2008

It would be helpful if all of this was on one thread, with replies 
embedded.  I have sent several replies to your questions, all of which 
have gone unacknowledged.  It makes it very difficult for anyone (myself 
or someone else) to give advice if we don't know what you're doing or 
what you've tried.  Even if something didn't work based on what I, or 
anyone else, tells you, it is nice to know that "I tried this, but I 
still have a problem, which is shown here: (exact error/warning/problem)."

As I've said before, exact procedural details of what you've done are 
essential for sorting out strange problems like this.  This means - 
*exact* (copy and paste) command lines from pdb2gmx, and any error 
messages you receive.  Also, any manipulations you have made to your 
input .pdb file.  It seems to me that you've probably edited your file 
to have only one chain identifier, and hence why pdb2gmx is trying to 
make everything one molecule.

The -merge option of pdb2gmx is what you want (see pdb2gmx -h).  If the 
following command line doesn't work, it would be nice to see an exact 
reason (i.e., copy/paste from the error/warning/whatever):

pdb2gmx -f (input).pdb -ignh -ter -merge

I got the above to work perfectly on an insulin structure I found in the 
RCSB (1ZNI), after deleting chains C and D from the .pdb file.  If your 
structure continues to give you headaches, try this one to make sure 
that your Gromacs installation is working properly (something I inquired 
about several days ago...)


rams rams wrote:
> 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 
> <mailto: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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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