[gmx-users] simulating two peptides in a box

Rakesh Mishra rakesh1986 at gmail.com
Mon Jul 7 20:13:59 CEST 2008 

Dear Justin,

 Here is the exact error message : ( Here I have tried to simulate 4 protein
molecules in a box ...basically I am looking at multiple molecule
interactions )

*grompp  -f em.mdp -c pep_sol.gro -o pep_em.tpr -p pep.top*

*checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 4
Excluding 2 bonded neighbours for SOL 8813
NOTE:
  System has non-zero total charge: 4.000000e+00

processing coordinates...
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "nt17.top", line 1126]:
  534 non-matching atom names
  atom names from nt17.top will be used
  atom names from nt17_sol.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   17626
#   G96BONDS:   716
#     ANGLES:   8813
#  G96ANGLES:   1040
#      PDIHS:   372
#      IDIHS:   320
#       LJ14:   1104
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat
There are:  8813      OTHER residues
There are:    68    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 27151 elements
Making dummy/rest group for Acceleration containing 27151 elements
Making dummy/rest group for Freeze containing 27151 elements
Making dummy/rest group for Energy Mon. containing 27151 elements
Making dummy/rest group for VCM containing 27151 elements
Number of degrees of freedom in T-Coupling group rest is 81450.00
Making dummy/rest group for User1 containing 27151 elements
Making dummy/rest group for User2 containing 27151 elements
Making dummy/rest group for XTC containing 27151 elements
Making dummy/rest group for Or. Res. Fit containing 27151 elements
Making dummy/rest group for QMMM containing 27151 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118
writing run input file...

Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4#
There was 1 warning*

Any suggestions would be appreciated .. Also I do believe that the order
might be a problem..but isnt an inclusion of the no .of molecules meant to
take care of that ?

Thanks

Rakesh




On Mon, Jul 7, 2008 at 10:50 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Several questions come to mind, aside from trying to sift through your
> interpretation of error messages.  Hint: always show your exact command,
> followed by the relevant portion of the screen output; that way we don't
> have to guess what you've been up to :-)
>
> 1. Do you have two different proteins, or are they the same?  If they are
> different, changing the number of Protein molecules in your topology will
> not be correct.  If they are the same, this is fine.
>
> 2. Does the order of your topology follow the order of the coordinate file?
>  When you get warnings about non-matching atom names, you should be alert
> that something has gone wrong.
>
> -Justin
>
> kartik mehra wrote:
>
>> Dear GMX Users,
>>
>> I am trying to set up a simulation box with two proteins. I have perused
>> the archives about the methodology of doing so. I tried the recommended
>> option of changing the number of protein molecules in the topology file to
>> 2. However when I run grompp after editconf and genbox, I get warning that
>> the number of co -ordinates do not match (since I had not updated the number
>> of solvent molecules ...) After updating the number of solvent molecules,
>> when I try running grompp again, it shows a warning that the 23644 atom
>> names do not match in top and gro files and that atom names from top files
>> are being chosen .
>>
>> Upon subsequent mdrun, the system explodes after a 1-4 interaction
>> warning.
>>
>> I was wondering whether anyone could help me out on this ... I do
>> understand that the topic has been discussed pretty often but would
>> appreciate any help ...
>>
>>
>> Cheers
>>
>> Kartik
>>
>> PS: I have not yet tried the other suggestion of translation and rotation
>> followed by concatenating the two files
>>
>>
>> ------------------------------------------------------------------------
>>
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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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