[gmx-users] Re: warning mesgs
rams rams
rams.crux at gmail.com
Mon Jun 30 19:45:03 CEST 2008
Hi,
I mistyped the command as you mentioned. I did used the following:
grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o
MM_insu.tpr
Now the error is the following:
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: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (insu_pwi2MM.pdb, 21149)
does not match topology (insu_pwi.top, 21157)
Ram.
On Mon, Jun 30, 2008 at 12:45 PM, Nuno Azoia <nazoia at det.uminho.pt> wrote:
> Hi!
>
> I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems to
> me that you forgot to create the required insu_pwi2MM.gro file. In your last
> pdb2gmx command you just created insu_pwi2MM.pdb, and then the last grompp
> command cannot found the insu_pwi2MM.gro file. I think you have to repeat
> the last pdb2gmx command in order to create the .gro file, something like
>
> pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter –merge
> -ignh
>
> (the same command you have written but with different output file)
>
> Nuno Azoia
>
> 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)
>>
>> 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<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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>>
>> ------------------------------------------------------------------------
>>
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>
>
> --
>
> Nuno Gonçalo Azoia Lopes
>
> Laboratório de Investigação em Acabamento
> Departamento de Engenharia Têxtil
> Universidade do Minho
> Campus de Azurém
> 4800-058 Guimarães
> Portugal
>
> Tel: +351 253 510 280 - Ext: 517 289
> Fax: +351 253 510 293
>
> Mobile: +351 965 382 487
> E-mail: nazoia at det.uminho.pt
>
>
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