Hi,<br><br>Let me explain what I did before posing the problem infront of you.<br><br>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.<br>
<br>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. <br><br>3. On this modified pdb file (x+y), i creaed the box and then neutralized using the following command:
<p class="MsoNormal"><b style="">genion -s MM_insu.tpr
-o insu_pwi.pdb -conc 0.008 –neutral <br></b></p><p class="MsoNormal">If I use -p option to write the top file, it says fatal error <b style="">insu_pwi.pdb. Its not writing this file.</b></p><p class="MsoNormal">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. <br>
</p>
<p class="MsoNormal"><b style=""><br></b></p><p class="MsoNormal"><b style="">4. Now I run grompp -f
eminimization.mdp -c insu_pwi2MM.pdb -p insu_p.top -o MM_insu.tpr</b></p><p class="MsoNormal">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.</p>
<br><p class="MsoNormal"></p>Ram.<br><br><p class="MsoNormal"><br></p>4. I run <br><br><br><br><div class="gmail_quote">On Tue, Jul 1, 2008 at 10:46 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The whole story continues to emerge... :-)<br>
<br>
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).<br>
<br>
-Justin<br>
<br>
rams rams wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>
Dear users,<br>
<br>
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:<br>
<br>
pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh<br>
<br>
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:<br>
<br>
Segmentation fault: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh<br>
<br>
It says like its creating the pdb and top files but nothing it could.<br>
<br>
The same command works fine if I remove -merge and its also worked well with insulin chains.<br>
<br>
I have enough space to run this too.<br>
<br>
Please let me know the suggestions.<br>
<br>
Ram.<br></div></div>
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========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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