[gmx-users] segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 2 20:08:43 CEST 2008
rams rams wrote:
> Hi,
>
> Let me explain what I did before posing the problem infront of you.
>
> 1. I started with my enzyme and processed it with pdb2gmx. I also
> processed my insulin with pdb2gmx (using -merge). I have two top files
> and the *.itp files corresponding to enzyme and insulin.
>
> 2. I copied the coordinates of insulin (_p.pdb) into the coordinates
> of the enzyme _p.pdb. I did changed the name of the insu_p.top to
> insu_p.itp and did added this to the _p.top file of my enzyme.
>
> 3. On this modified pdb file (x+y), i creaed the box and then
> neutralized using the following command:
>
> *genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral
> *
>
> If I use -p option to write the top file, it says fatal error
> *insu_pwi.pdb. Its not writing this file.*
>
It is *always* better to do an exact copy-paste of the error message
(and any relevant screen output) so we can help in diagnosing the problem.
Probably your box is not large enough to accommodate such a small
concentration (8 mM). Is that what you want? It looks like with 62 Na+
and 39 Cl- your box would have to be astronomically large. For a
typical protein in water that would probably be about 8 M, not 8 mM!
Test things out just by using the genion -neutral option, before trying
to add anything extra. That way you can make sure things are working
properly on a basic level.
> then I did tried adding the ions manually. I did added 62 Na and 39 Cl
> ions. then it creaed the insu_pwi.pdb file and then made the
> corresponding changes in the _p.top file. I did removed the
> corresponding number of water molecuels from SOL and added Na and Cl
> numbers.
>
> *
> *
>
> *4. Now I run grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p
> insu_p.top -o MM_insu.tpr*
>
> it says the total charge of the system is -2. Though I used the
> correct number of ions. while processing initial pdb2gmx, my protein
> has -21 charge and insulin has -2 charge. So with 62 Na and 39 Cl, I
> added total 23 Na ions. but still it says -2 is the charge. Am I
> making any mistake in the process.
>
>
Never proceed when a simple program like genion has a problem. Setup
tools are generally very reliable, and if they don't work, it suggests
something else is badly wrong with what you tried to do. Not always
true, but in general, stop and think before trying to plow ahead :-)
-Justin
> Ram.
>
>
> 4. I run
>
>
>
> On Tue, Jul 1, 2008 at 10:46 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
> The whole story continues to emerge... :-)
>
> You're probably experiencing this problem because you're trying to
> process two separate proteins with one pdb2gmx command. You will
> need to separate (i.e., using a text editor) chain A (whatever
> protein) from B&C (insulin). Process them separately with
> pdb2gmx, using -merge with the insulin portion. What you'll have
> to do is then concatenate the output structure files (again, text
> editor or Unix 'cat' command), and include the insulin topology
> within the topol.top from Protein A. See Chapter 5 of the manual
> for more details on this, but it is essentially analogous to
> including a ligand topology (.itp) within a system topology (.top).
>
> -Justin
>
> rams rams wrote:
>
> Dear users,
>
> Thanks a lot to Justin and a few others who really helped me
> in successfully running insulin. Now, I am trying to setup
> the input file for insulin with other enzyme and I am trying
> to merge the two chains of insulin. I am using the following
> command:
>
> pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge
> -ignh
>
> it is asking whether to merge (A &B, B&C). I allowed it to
> merge B&C they are insulin chains and A is the rest of the
> enzyme. With the above command after adding all the protons to
> LYS etc.., it complains the folling:
>
> Segmentation fault: pdb2gmx -f insu.pdb -p insu_p.top -o
> insu_p.pdb -inter -merge -ignh
>
> It says like its creating the pdb and top files but nothing it
> could.
>
> The same command works fine if I remove -merge and its also
> worked well with insulin chains.
>
> I have enough space to run this too.
>
> Please let me know the suggestions.
>
> Ram.
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> ========================================
>
> 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
>
> ========================================
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
========================================
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
========================================
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list