[gmx-users] segmentation fault

[rams rams]

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.*

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.

Ram.


4. I run



On Tue, Jul 1, 2008 at 10:46 AM, Justin A. Lemkul <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.
>> ------------------------------------------------------------------------
>>
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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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