[gmx-users] Ammonia in Water

[chris.neale at utoronto.ca]

First, I doubt that you want a molecule with a partial charge.

Second, just because the bonds, angles, and LJ parameters will be  
generated doesn't mean they will be correct. What are the N-H bond  
lengths of ammonia? Are those the same as the ones that you are  
including here? Take a look at ffoplsaabon.itp and, for LJ parameters,  
ffoplsaanb.itp.

Third, ammonia has a lone pair if memory serves. Are your angles  
sufficient to reproduce the geometry? i.e. will you get the correct  
pyramidal structure or will you perhaps get a planar structure? Hint:  
I think that your topology will pick up the following angles from  
ffoplsaabon.itp

   H      N      H       1   120.000    292.880   ; ADE,CYT,GUA,GLN,ASN     **

Finally, it is often said -- though rarely heard -- that  
parameterization is a very advanced topic best attempted after you  
have sufficient simulation experience:
http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization&highlight=exotic



> Hello,
>
>     I created a topology file for 1 ammonia in water. Could someone
> please have a look at the file and let me know if it looks okay.
>
> Thanks
> Nisha Patel
>
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> Ammonia             3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
>       1   opls_237      1    NH3      N      1      -0.76    14.0067
> ; qtot -0.76
>       2   opls_240      1    NH3     H1      1       0.38      1.008
> ; qtot -0.38
>       3   opls_240      1    NH3     H2      1       0.38      1.008  
>    ; qtot 0
>       4   opls_240      1    NH3     H3      1       0.38      1.008
> ; qtot 0.38
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      1     2     1
>      1     3     1
>      1     4     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
>        c3
>      2     1     3     1
>      2     1     4     1
>      3     1     4     1
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
>
> [ system ]
> ; Name
> ammonia in water
>
> [ molecules ]
> ; Compound        #mols
> Ammonia             1
> SOL               345
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 15 Jan 2010 21:26:47 +0530 (IST)
> From: "P.R.Anand Narayanan" <nandu_cooldevil at yahoo.co.in>
> Subject: [gmx-users] polymer-protein
> To: gromacs <gmx-users at gromacs.org>
> Message-ID: <61710.4449.qm at web95203.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Gromacs users,
>
> I have to attach a chemical polymer to a protein and when I created   
> peptide bonds and saved it, the entire format of the pdb file   
> changed. That is the entire identity of the protein was lost and the  
>  pdb file was saved in the form of ATOMS and not residues.
> Are there any solutions to this or can I Use the same in   
> gromacs??????? If yes, how can I use it in the pdb2gmx command????
>
> Please help,
> Thanking you,
> regards,
> Anand
>
>
>       The INTERNET now has a personality. YOURS! See your Yahoo!   
> Homepage. http://in.yahoo.com/
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> Message: 5
> Date: Fri, 15 Jan 2010 17:06:25 +0100
> From: Baofu Qiao <qiaobf at gmail.com>
> Subject: [gmx-users] implicit wall doesn't recognize the wall_atomtype
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