[gmx-users] bug in editconf for making a box ? combined two residues into one

[maria goranovic]

Thanks for the replies. I guess it is a very small bug. However, here is
another:

I have a 2-protein complex in water. The first protein residues numbers are
from residues 4 to 14, and the other from 5 to 9. In the INPUT .gro file to
grompp, I have a continuous numbering of residues from 4 to 19 (4 to 14+5).
However, after an energy minimization, gromacs writes out a .gro file which
preserves the original numbering (4 to 14 and 5 to 9) instead of a numbering
from 4 to 19. Why does it do that? I can see the problem with such a
numbering because I can never unambiguously select "residue number 6" if I
want to make an index file. How does one go about fixing this?

I made the original input .gro file by using : editconf -f in.gro -o out.gro
-resnr 4

In the topology file, I read in protein_A.itp and protein_B.itp which start
from the original pdb residue number (4 and 5 respectively for the two
chains)

Thank you for helping,

Maria



On Wed, Aug 3, 2011 at 3:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> maria goranovic wrote:
>
>> Hi
>>
>> I am using editconf to set my box to the right size using:
>>
>> editconf -f in.gro -o out.gro -box 30 30 30
>>
>> gromacs v. 4.5.3
>>
>> For this example, my system contains a phosphate anion and a water
>> molecule. After editconf runs, it changes the residue name SOL of the water
>> molecule to the residue name PHO for phosphate, because both have the same
>> residue number (1). Is this not a bug, or am I doing something really silly?
>> One can always try to run a simulation of an amino acid in water, and the
>> error below would be replicated?
>>
>
> I suspect so.  You can file a bug report, but it will probably remain a
> very low priority for now.  One normally does not number a coordinate file
> this way. Each residue should be numbered independently.
>
>
>  Interestingly, grompp does not complain that the residue PHO has 8 atoms
>> instead of 5 as in the topology file.
>>
>>
> AFAIK grompp only pays attention to atom names, which in this case likely
> match the topology without an issue.
>
> -Justin
>
>
>  I do not see this problem if the residue number of the water molecule is 2
>> instead of 1.
>>
>> Below are the two .gro files, before and after running the above command.
>>
>>
>> GROtesk MACabre and Sinister
>> 8
>>    1PHO    O1P    1  13.422   2.753   5.900
>>    1PHO      P    2 13.250 2.818   5.976
>>    1PHO    O2P    3  13.193   2.967   5.853
>>    1PHO    O3P    4 13.263 2.864   6.169
>>    1PHO    O4P    5  13.118   2.672   5.939
>>    1SOL     OW    1  12.025   1.421  -1.203
>>    1SOL    HW1    2  12.125   1.421  -1.203
>>    1SOL    HW2    3  11.993   1.516  -1.203
>> 20 20 20
>>
>>
>> GROtesk MACabre and Sinister
>>    8
>>    1PHO    O1P    1  15.623  15.449  17.622
>>    1PHO      P    2  15.451  15.514  17.697
>>    1PHO    O2P    3  15.394  15.663  17.574
>>    1PHO    O3P    4  15.464  15.560  17.890
>>    1PHO    O4P    5  15.319  15.368  17.660
>>    1PHO     OW    6  14.226  14.117  10.518
>>    1PHO    HW1    7  14.326  14.117  10.518
>>    1PHO    HW2    8  14.194  14.212  10.518
>>  30.00000  30.00000  30.00000
>>
>>
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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