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

[Justin A. Lemkul]

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

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