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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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interface or send it to [EMAIL PROTECTED]
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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
========================================
--
========================================
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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