Hi,<br><br>I mistyped the command as you mentioned. I did used the following:<br><br>grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o MM_insu.tpr<br><br>Now the error is the following:<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: grompp.c, line: 448<br>
<br>Fatal error:<br>number of coordinates in coordinate file (insu_pwi2MM.pdb, 21149)<br> does not match topology (insu_pwi.top, 21157)<br><br>Ram.<br><br><br><div class="gmail_quote">On Mon, Jun 30, 2008 at 12:45 PM, Nuno Azoia <<a href="mailto:nazoia@det.uminho.pt">nazoia@det.uminho.pt</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;">Hi!<br>
<br>
I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems to me that you forgot to create the required insu_pwi2MM.gro file. In your last pdb2gmx command you just created insu_pwi2MM.pdb, and then the last grompp command cannot found the insu_pwi2MM.gro file. I think you have to repeat the last pdb2gmx command in order to create the .gro file, something like<br>
<br>
pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter –merge -ignh<br>
<br>
(the same command you have written but with different output file)<br>
<br>
Nuno Azoia<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><div></div><div class="Wj3C7c">
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>
pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge<br>
<br>
(since I removed all the hydrogens in my starting insu.pdb so didnt used -ignh here)<br>
<br>
editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0<br>
<br>
genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top<br>
<br>
grompp -f eminimization.mdp -c insu_pw.pdb -p insu_p.top -o MM_insu.tp<br>
<br>
genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral<br>
<br>
pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter –merge -ignh<br>
<br>
grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o MM_insu.tpr<br>
<br>
<br>
<br>
The following is the error:<br>
<br>
<br>
<br>
<br>
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></div><div><div></div><div class="Wj3C7c">
On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
It would be helpful if all of this was on one thread, with replies<br>
embedded. I have sent several replies to your questions, all of<br>
which have gone unacknowledged. It makes it very difficult for<br>
anyone (myself or someone else) to give advice if we don't know<br>
what you're doing or what you've tried. Even if something didn't<br>
work based on what I, or anyone else, tells you, it is nice to<br>
know that "I tried this, but I still have a problem, which is<br>
shown here: (exact error/warning/problem)."<br>
<br>
As I've said before, exact procedural details of what you've done<br>
are essential for sorting out strange problems like this. This<br>
means - *exact* (copy and paste) command lines from pdb2gmx, and<br>
any error messages you receive. Also, any manipulations you have<br>
made to your input .pdb file. It seems to me that you've probably<br>
edited your file to have only one chain identifier, and hence why<br>
pdb2gmx is trying to make everything one molecule.<br>
<br>
The -merge option of pdb2gmx is what you want (see pdb2gmx -h).<br>
If the following command line doesn't work, it would be nice to<br>
see an exact reason (i.e., copy/paste from the<br>
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<br>
in the RCSB (1ZNI), after deleting chains C and D from the .pdb<br>
file. If your structure continues to give you headaches, try this<br>
one to make sure that your Gromacs installation is working<br>
properly (something I inquired about several days ago...)<br>
<br>
-Justin<br>
<br>
rams rams wrote:<br>
<br>
HI,<br>
<br>
When I use the merge command along with pdb2gmx to form inter<br>
disulphide bonds between two different chains, its removing a<br>
water molecule to connect the two ends. Its like forming a<br>
peptide bond which I dont wish. Is there any way to tell to<br>
gromacs, to create the inter dishulphide bonds without<br>
creating the peptide bond between the two chains ?<br>
<br>
<br>
<br>
On Fri, Jun 27, 2008 at 6:51 PM, rams rams<br>
<<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>><br></div></div><div><div></div><div class="Wj3C7c">
<mailto:<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>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
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</div></blockquote>
<br>
<br>
-- <br>
<br>
Nuno Gonçalo Azoia Lopes<br>
<br>
Laboratório de Investigação em Acabamento<br>
Departamento de Engenharia Têxtil<br>
Universidade do Minho<br>
Campus de Azurém<br>
4800-058 Guimarães<br>
Portugal<br>
<br>
Tel: +351 253 510 280 - Ext: 517 289<br>
Fax: +351 253 510 293<br>
<br>
Mobile: +351 965 382 487<br>
E-mail: <a href="mailto:nazoia@det.uminho.pt" target="_blank">nazoia@det.uminho.pt</a><div><div></div><div class="Wj3C7c"><br>
<br>
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