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
