rams rams wrote:
Dear Justin,
I am absolutely sorry for the discomfort. Since this is the first time
I am using Gromacs, so things are not clear to me so I am trying
things very randomly thats why I could not keep update the things.
Here I restarted every thing and have a look at and let me know your
suggestions:
pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge
(since I removed all the hydrogens in my starting insu.pdb so didnt
used -ignh here)
Well, assuming you have all the correct hydrogens in the right place,
that's fine, but in general, it is very easy to let pdb2gmx do the work
for you and use -ignh. If it generated the topology for you, then
that's fine.
editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0
genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top
grompp -f eminimization.mdp -c insu_pw.pdb -p insu_p.top -o MM_insu.tp
genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral
pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter
–merge -ignh
Here's where your problem is. This step is unnecessary! Once you have
the topology, there is no need to re-process with pdb2gmx. Once you
have added solvent and ions, simply make the changes to your topology
with a text editor.
grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
MM_insu.tpr
It has already been correctly pointed out by another user that you
specified -o .pdb in the above step, but then called for the .gro
equivalent here. That would be a problem.
Basically, once the genion step is done, and you have made the
appropriate changes to the topology (which can also be done with the -p
flag of genion), then proceed to grompp.
This makes much more sense, and it is easier to get help when it is
clearly presented like this!
-Justin
The following is the error:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6878
turning all bonds into constraints...
NOTE:
System has non-zero total charge: -2.000000e+00
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: futil.c, line: 340
File input/output error:
insu_pwi2MM.gro
Ram.
On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
It would be helpful if all of this was on one thread, with replies
embedded. I have sent several replies to your questions, all of
which have gone unacknowledged. It makes it very difficult for
anyone (myself or someone else) to give advice if we don't know
what you're doing or what you've tried. Even if something didn't
work based on what I, or anyone else, tells you, it is nice to
know that "I tried this, but I still have a problem, which is
shown here: (exact error/warning/problem)."
As I've said before, exact procedural details of what you've done
are essential for sorting out strange problems like this. This
means - *exact* (copy and paste) command lines from pdb2gmx, and
any error messages you receive. Also, any manipulations you have
made to your input .pdb file. It seems to me that you've probably
edited your file to have only one chain identifier, and hence why
pdb2gmx is trying to make everything one molecule.
The -merge option of pdb2gmx is what you want (see pdb2gmx -h).
If the following command line doesn't work, it would be nice to
see an exact reason (i.e., copy/paste from the
error/warning/whatever):
pdb2gmx -f (input).pdb -ignh -ter -merge
I got the above to work perfectly on an insulin structure I found
in the RCSB (1ZNI), after deleting chains C and D from the .pdb
file. If your structure continues to give you headaches, try this
one to make sure that your Gromacs installation is working
properly (something I inquired about several days ago...)
-Justin
rams rams wrote:
HI,
When I use the merge command along with pdb2gmx to form inter
disulphide bonds between two different chains, its removing a
water molecule to connect the two ends. Its like forming a
peptide bond which I dont wish. Is there any way to tell to
gromacs, to create the inter dishulphide bonds without
creating the peptide bond between the two chains ?
On Fri, Jun 27, 2008 at 6:51 PM, rams rams
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
Hi,
I have three di sulphide bonds in my crystal structure. In the
topology file it left blanks at the corresponding sulphur
connectivities (i.e., values corresponding to gb_, ga_. gd_ ).
When I try to create the .tpr file it complains the following:
processing topology...
Generated 716 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1046 of the 2628 1-4 parameter combinations
WARNING 1 [file "insu_pwi.top", line 607]:
No default G96Bond types, using zeroes
WARNING 2 [file "insu_pwi.top", line 745]:
No default G96Bond types, using zeroes
WARNING 3 [file "insu_pwi.top", line 2008]:
No default G96Angle types, using zeroes
WARNING 4 [file "insu_pwi.top", line 2209]:
No default G96Angle types, using zeroes
WARNING 5 [file "insu_pwi.top", line 2345]:
No default G96Angle types, using zeroes
WARNING 6 [file "insu_pwi.top", line 2512]:
No default G96Angle types, using zeroes
WARNING 7 [file "insu_pwi.top", line 2748]:
No default Proper Dih. types, using zeroes
WARNING 8 [file "insu_pwi.top", line 2820]:
No default Proper Dih. types, using zeroes
WARNING 9 [file "insu_pwi.top", line 2863]:
No default Proper Dih. types, using zeroes
WARNING 10 [file "insu_pwi.top", line 2919]:
No default Proper Dih. types, using zeroes
Cleaning up temporary file gromppID2O6e
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: fatal.c, line: 416
Fatal error:
Too many warnings, /usr/local2/gromacs/bin/grompp terminated
-------------------------------------------------------
"Encountered Subspace Anomaly" (Star Trek)
MD_insu.tpr was not created. Check for errors. Exiting ...
Is there a way to fix it ? Also what are those b_, ga_. gd_
corresponds to ??
Ram.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[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]
<mailto:[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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[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]
<mailto:[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
