[gmx-users] Re: warning mesgs
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 30 19:44:01 CEST 2008
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)
Well, assuming you have all the correct hydrogens in the right place,
that's fine, but in general, it is very easy to let pdb2gmx do the work
for you and use -ignh. If it generated the topology for you, then
that's fine.
> 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
>
Here's where your problem is. This step is unnecessary! Once you have
the topology, there is no need to re-process with pdb2gmx. Once you
have added solvent and ions, simply make the changes to your topology
with a text editor.
> grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
> MM_insu.tpr
>
>
It has already been correctly pointed out by another user that you
specified -o .pdb in the above step, but then called for the .gro
equivalent here. That would be a problem.
Basically, once the genion step is done, and you have made the
appropriate changes to the topology (which can also be done with the -p
flag of genion), then proceed to grompp.
This makes much more sense, and it is easier to get help when it is
clearly presented like this!
-Justin
>
> 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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--
========================================
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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