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...)
-Justin
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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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