Dear Justin,<br><br>I am absolutely sorry for the discomfort. Since this is the first time I am using Gromacs, so things are not clear to me so I am trying things very randomly thats why I could not keep update the things. Here I restarted every thing and have a look at and let me know your suggestions:<br>
<br>
<p class="MsoNormal">pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge </p>
(since I removed all the hydrogens in my starting insu.pdb so didnt used -ignh here)
<p class="MsoNormal">editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0
-center 3.0 3.0 3.0</p>
<p class="MsoNormal">genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p
insu_p.top</p>
<p class="MsoNormal">grompp -f eminimization.mdp -c<span style=""> </span>insu_pw.pdb -p insu_p.top -o MM_insu.tp</p>
<p class="MsoNormal">genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral</p>
<p class="MsoNormal">pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb
-inter –merge -ignh</p><p class="MsoNormal">
</p><p class="MsoNormal">grompp -f eminimization.mdp -c insu_pwi2MM.gro -p
insu_pwi.top -o MM_insu.tpr</p><br><p class="MsoNormal"><br></p><p class="MsoNormal">The following is the error:</p><br><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#<br>checking input for internal consistency...<br>calling /lib/cpp...<br>processing topology...<br>Generated 716 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 1<br>
Generated 1046 of the 2628 1-4 parameter combinations<br>Excluding 3 bonded neighbours for Protein 1<br>turning all bonds into constraints...<br>Excluding 2 bonded neighbours for SOL 6878<br>turning all bonds into constraints...<br>
NOTE:<br> System has non-zero total charge: -2.000000e+00<br><br>processing coordinates...<br>-------------------------------------------------------<br>Program grompp, VERSION 3.3.1<br>Source code file: futil.c, line: 340<br>
<br>File input/output error:<br>insu_pwi2MM.gro<br><br><br>Ram.<br><br><br><br><br><br><div class="gmail_quote">On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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)."<br>
<br>
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.<br>
<br>
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):<br>
<br>
pdb2gmx -f (input).pdb -ignh -ter -merge<br>
<br>
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...)<br>
<br>
-Justin<br>
<br>
rams rams wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
HI,<br>
<br>
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 ?<br>
<br>
<br>
<br></div><div><div></div><div class="Wj3C7c">
On Fri, Jun 27, 2008 at 6:51 PM, rams rams <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a> <mailto:<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>>> wrote:<br>
<br>
Hi,<br>
<br>
I have three di sulphide bonds in my crystal structure. In the<br>
topology file it left blanks at the corresponding sulphur<br>
connectivities (i.e., values corresponding to gb_, ga_. gd_ ).<br>
When I try to create the .tpr file it complains the following:<br>
<br>
processing topology...<br>
Generated 716 of the 2628 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 1<br>
Generated 1046 of the 2628 1-4 parameter combinations<br>
WARNING 1 [file "insu_pwi.top", line 607]:<br>
No default G96Bond types, using zeroes<br>
WARNING 2 [file "insu_pwi.top", line 745]:<br>
No default G96Bond types, using zeroes<br>
WARNING 3 [file "insu_pwi.top", line 2008]:<br>
No default G96Angle types, using zeroes<br>
WARNING 4 [file "insu_pwi.top", line 2209]:<br>
No default G96Angle types, using zeroes<br>
WARNING 5 [file "insu_pwi.top", line 2345]:<br>
No default G96Angle types, using zeroes<br>
WARNING 6 [file "insu_pwi.top", line 2512]:<br>
No default G96Angle types, using zeroes<br>
WARNING 7 [file "insu_pwi.top", line 2748]:<br>
No default Proper Dih. types, using zeroes<br>
WARNING 8 [file "insu_pwi.top", line 2820]:<br>
No default Proper Dih. types, using zeroes<br>
WARNING 9 [file "insu_pwi.top", line 2863]:<br>
No default Proper Dih. types, using zeroes<br>
WARNING 10 [file "insu_pwi.top", line 2919]:<br>
No default Proper Dih. types, using zeroes<br>
Cleaning up temporary file gromppID2O6e<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.1<br>
Source code file: fatal.c, line: 416<br>
<br>
Fatal error:<br>
Too many warnings, /usr/local2/gromacs/bin/grompp terminated<br>
-------------------------------------------------------<br>
<br>
"Encountered Subspace Anomaly" (Star Trek)<br>
<br>
MD_insu.tpr was not created. Check for errors. Exiting ...<br>
<br>
Is there a way to fix it ? Also what are those b_, ga_. gd_<br>
corresponds to ??<br>
<br>
Ram.<br>
<br>
<br></div></div><div class="Ih2E3d">
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
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