[gmx-users] Re: Inquiry Again.

[Anton Feenstra]

Albert Sun wrote:
> Dear Anton and Gmx-users,
>  
> If without bonds, I think the top file (as shown in urea.top - manual page 100) will like this:

First off, but I'm not 100% sure, the .top starts with an obligatory
[defaults] section, indicating things like exclusions along bonds (not
relevant for you) and LJ combination rules. Check the manual.

> [moleculetype] ... [atom] ... [bonds]  ; no need to input

Looks good up to here, but I don't see where you need [pairs]. These are
normally used as a modification to a dihedral potential, i.e. the LJ
interaction for the 1-4 pair on a dihedral angle should often be less
than the normal LJ interaction.

> [pairs]
> ;ai       aj        funct           b0       kb
[...]
> [angles]  ;  no need to input ... [dihedrals];  no need to input 

Looks good again, but for position restraint one usually wants a switch
to turn them on or off, so you in stead of:

> [position_restraints}
> 1    1    1000     1000    10000
> ...

You would put:
#ifdef POSRES
[position_restraints]
1    1    1000   1000   1000
...
#endif

using a switch in your .mdp file like 'defines = -DPOSRES'

> ... #include  "spc.itp" ... [system] ... [molecules] ...

Looks good again.

> Besides, how could we select ' without bonds'  when we do pdb2gmx or by modifying 
> .pdb file ?

No, no! pdb2gmx is for *building* *topologies*, mainly for biopolymers
like proteins or DNA. If you build your own topology, or use one from
e.g. ProDrg, you *do* *not* *need* pdb2gmx! My apologies if I seem too
explicit here, but I see many people using pdb2gmx when it is not
necessary, which often causes all kinds of terrible problems, not to
mention a lot of unnecessary work!

So, if you build your topology (= .top file), you will not have any
bonds. You should use your .gro (or .pdb) file with coordinates and
.top file with topology directly as input to grompp (and an .mdp file
of course). No bonds in your .top file = no bonds in your .tpr file!

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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