[gmx-users] protein-ligand complex tutorial

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> You prepared a useful tutorial. if you used PO4 ligand (which has 2 
> molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and 
> .gro files of ligand because of 2 molecule, what change?
> Can you give some hint?

Treat it like you would any other component of the system - build an .itp file 
for PO4 and add:

PO4  2

to your [molecules] directive.

-Justin

> Thanks
> 
> 3HTB.pdb
> ....
> 
> TER 1365 ASN A 163
> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P
> HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O
> HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O
> 
> HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O
> HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O
> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P
> HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O
> 
> HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O
> HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O
> HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O
> HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C
> 
> ..
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 

-- 
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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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