[gmx-users] residue name changes "SOL" to "HOH"

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
>  I have a .pdb file for water modecules.
>  When I run pdf2gmx command residure name "SOL" change "HOH". I am using
> opls force field parameters.
> Can you tell whats the problem.

There is no problem, per se.  It appears that (in the latest version of the code 
around line 1298 of pdb2gmx.c), pdb2gmx renames all water models "HOH" unless 
they are TIP4P or TIP5P.  Whether or not this is appropriate is another matter, 
since all water .itp files (regardless of force field) appear to refer to water 
as "SOL."

A lot of code changes have occurred in an effort to streamline topology 
production.  Please report back if this actually causes a problem later down the 
line so it can be properly investigated before the release of version 4.5. 
Also, make sure to always refer to the version you are using.  Since development 
has been very rapid lately, changes are occurring all the time.

-Justin

> Here is my .pdb dfile
> 
> TITLE     Protein in water
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   30.273   30.273   30.273  90.00  90.00  90.00 P 1           1
> MODEL        1
> ATOM      1  OW  SOL     1      30.029  25.981  28.726  1.00  0.00
> ATOM      2  HW1 SOL     1      30.271  25.107  28.304  1.00  0.00
> ATOM      3  HW2 SOL     1      30.216  26.725  28.084  1.00  0.00
> ATOM      4  OW  SOL     2      14.532   6.560  16.036  1.00  0.00
> 
> 
> ATOM   2591  HW1 SOL   864       5.172   6.310  18.849  1.00  0.00
> ATOM   2592  HW2 SOL   864       6.771   6.137  19.128  1.00  0.00
> TER
> ENDMDL
> NIlesh
> 
> 

-- 
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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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