[gmx-users] Re: warning mesgs

rams rams rams.crux at gmail.com
Mon Jun 30 18:29:39 CEST 2008 

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)

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

grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o
MM_insu.tpr


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 <jalemkul at vt.edu> 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 <rams.crux at gmail.com <mailto:
>> rams.crux at gmail.com>> 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.
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> 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
>
> ========================================
>
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