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 <[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. >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [EMAIL PROTECTED] >> 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 > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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