Please make sure you're including the gmx-users listserv on your
replies. That way, others can weigh in; they may have better ideas than me!
So what you're saying, is if you give: "pdb2gmx -f input.pdb -merge" you
get the error you mentioned before:
Fatal Error:
Atom H1 in residue PHE 22 not found in rtp entry with 17 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
Is that correct? If so, it seems like someone has been playing with
your .hdb or .rtp files. If you have no H atoms in your input, then
something else very weird is going on...
-Justin
rams rams wrote:
Dear Justin,
Thanks for your quick replies. But in my starting input pdb I am not
keeping any of the Hydrogen atoms. I have only the heavy atoms in my
pdb to start with. All the hydrogens are added by the gromacs. Also I
didnt face this problem when I am treating the two chains as separate
one (i.e., if i am not using -merge command ofcourse in that case I
couldnt see any inter disulphide bonds).
Ram.
On Thu, Jun 26, 2008 at 8:33 PM, Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
rams rams wrote:
Hi,
If I use -ignh, that will ignore all the hydrogens in my
input. And these hydrogens are added by the gromacs.in
<http://gromacs.in> <http://gromacs.in> the first step of
creating the top file.
What is gromacs.in <http://gromacs.in>? Perhaps it would be best
if you showed us, step by step, what you are doing (with *exact*
command lines).
Using pdb2gmx should be your first step, and using -ignh will
indeed ignore your hydrogen atoms, but it looks like they're named
incorrectly anyway, so that might be a good thing. Part of the
function of pdb2gmx is to add back the appropriate hydrogens
according to residue templates, so it's irrelevant what you have
in the input; it's going to be replaced with correct hydrogen
atoms anyway.
-Justin
Ram.
On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
rams rams wrote:
Dear Tsjerk,
Thanks for the suggestion but when I use -merge command it
says segmentation error. Let me put the problem in a more
elaborated way.
I am running this simulation on insulin. It has two
chains "a"
and "b" which are independent fragments but there are two
inter disulphide bonds between the two chains. If I
keep the
two chains as a single molecule (as -merge command does)
gromacs could recognize the inter dishlphide bonds but
while
running the following error appears:
396 398 113.3 0.1470 0.2974 0.1470
398 399 93.1 0.1530 0.4267 0.1530
399 400 45.5 0.1230 0.1693 0.1230
399 401 46.5 0.1330 0.1881 0.1330
Step= 2, Dmax= 5.0e-03 nm, Epot= -3.06153e+22 Fmax=
inf, atom= 25
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each
particle
to a grid
based on its coordinates. If your system contains
collisions
or parameter
errors that give particles very high velocities you
might end
up with some
coordinates being +-Infinity or NaN (not-a-number).
Obviously,
we cannot
put these on a grid, so this is usually where we detect
those
errors.
Make sure your system is properly energy-minimized and that
the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been
within
[ 0 .. 1000 ]
Please report this to the mailing list
([email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> <mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>)
When do you get this error (i.e., minimization, equilibration,
production)? Usually this type of error comes up from a poorly
minimized/equilibrated structure.
I agree with Tsjerk that using -merge is the right way to form
your disulfide, so I assume something else is going wrong
during
your system preparation. If you'd like to provide details
on what
you're doing in terms of minimization/equilibration, and the
contents of the relevant .mdp files, we may be able to detect
problems.
-Justin
Where as, if I keep these two as separate molecules it
couldnt
recognize the two inter disulphide bonds but its
running. Now
it is adding hydrogens to the sulhur atoms.
Is there any way to fix this problem ? Is there any way to
edit the topology file to remove the added hydrogen atoms ?
Thanks
Ram.
On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>> wrote:
Hi Ram,
Check the option -merge of pdb2gmx.
Cheers,
Tsjerk
On Thu, Jun 26, 2008 at 6:11 AM, rams rams
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>>
wrote:
> Dear Gromacs users,
>
> Is there any way to handle the disulphide bond formed
between two
> independent fragments of a protein ? Precisely it
is an inter
disulphide
> bond between two fragments. If I keep the two
fragments as
separate objects
> while preparing the pdb file (using TER between
the two
fragments), gromacs
> is not asking for the formation of a disulphide
bond. If
I keep
them as a
> single object while preparing the input pdb,
gromacs could
recognize the
> disulphide bond but while running the energy
minimization its
complaining
> that the distances are too close.
>
> Is there any way to handle these ? I am also thinking
like keep
them as
> separate objects and imposing positional restraints on
both the
sulphur
> atoms. Is it all right to do that way ?
>
> Please suggest me some thing how to handle these ?
>
> Ram.
>
> _______________________________________________
> gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[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]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>.
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[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]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[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]>
<mailto:[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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[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]>
<mailto:[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
========================================
--
========================================
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
