[gmx-users] Re: warning mesgs
Nuno Azoia
nazoia at det.uminho.pt
Mon Jun 30 18:45:45 CEST 2008
Hi!
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
pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter
–merge -ignh
(the same command you have written but with different output file)
Nuno Azoia
rams rams wrote:
> Dear Justin,
>
> 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:
>
> pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge
>
> (since I removed all the hydrogens in my starting insu.pdb so didnt
> used -ignh here)
>
> editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0
>
> genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top
>
> grompp -f eminimization.mdp -c insu_pw.pdb -p insu_p.top -o MM_insu.tp
>
> genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral
>
> pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter
> –merge -ignh
>
> grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
> MM_insu.tpr
>
>
>
> The following is the error:
>
>
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> checking input for internal consistency...
> calling /lib/cpp...
> 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
> Excluding 3 bonded neighbours for Protein 1
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 6878
> turning all bonds into constraints...
> NOTE:
> System has non-zero total charge: -2.000000e+00
>
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: futil.c, line: 340
>
> File input/output error:
> insu_pwi2MM.gro
>
>
> Ram.
>
>
>
>
>
> On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
> 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
> <rams.crux at gmail.com <mailto:rams.crux at gmail.com>
> <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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>
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--
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt
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