[gmx-users] Re: warning mesgs
rams rams
rams.crux at gmail.com
Mon Jun 30 19:55:01 CEST 2008
is that fine if i change the SOL number in the top file created at the first
step ?
On Mon, Jun 30, 2008 at 1:50 PM, rams rams <rams.crux at gmail.com> wrote:
> 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.
>
> Could you explain what changes I should make in the topology file ??
>
>
>
>
> On Mon, Jun 30, 2008 at 1:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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 <jalemkul at vt.edu<mailto:
>>> 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>
>>> <mailto: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 <http://vt.edu> | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>> _______________________________________________
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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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