[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa

[Abil Aliev]

just to summarise, the following works:

pdb2gmx -ff oplsaa -water tip4p -f sum.pdb -p speptide -o speptide
vi speptide.gro
 :%s/ OW/MW1     ; OW and HW3 have the same xyz
 :%s/HW3/OW4
 :%s/HW2/HW3
 :%s/HW1/HW2
 :%s/HO4/SOL
editconf, then
genbox -cp out -cs tip4p.gro -o b4em -p speptide
vi em.mdp
 define = -DPOSRES_WATER
 constraints         =  none
 integrator          =  steep
 nsteps              =  100
grompp, then mpirun c0-1 mdrun_d  -v -s em -o em -c after_em -g emlog
    ...
  Potential Energy  = -193192
  Maximum force     =  1676


> David wrote:
>
>>On Wed, 2004-12-15 at 16:44 +0000, Abil Aliev wrote:
>>  
>>
>>>thanks, David. what about 2 different types of tip4p:
>>>"pdb2gmx -ff oplsaa -water tip4p" results in HO4 with HW1 for 
>>>crystallographic water, whereas "genbox -cs tip4p" gives MW1 for the 
>>>added water molecules (the other 3 atoms are the same). in fact, without 
>>>manually editing the gro file grompp simply fails, complaining about 
>>>different number of atoms in top and gro files.
>>>    
>>>
>>Since you have discovered this, you can probably fix it too :).
>>
>>Some MD equilibration will fix all your problems in this respect.
>>  
>>
>>>>with the above i get OW1,HW1,HW2 and HW4 for crystallogrphic waters 
>>>>which are labelled as HO4. after editconf/genbox -cs tip4p i get a 
>>>>different type for added water with HW1 above replaced by MW1. i can 
>>>>change HW1 to MW1 and HO4 to HOH before genbox to get the grompp 
>>>>working, but is this the right way to proceed?
>>>>      
>>>>
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>>>    
>>>
>
>------------------------------------------------------------------------
>
>  
>

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