[gmx-users] GTG to GAG with amber FF99SB force field

[yaolisha at msu.edu]

Hi Tsjerk,
    Thank you for the response. I am sorry for the bad email structure  
which was messed up when I copy it from microsoft word to my email  
editor.
    The error message from gromacs i think comes from the multiplicity  
of HA-CA-CB-OH dihedral. In amber ff99sb force field, this dihedral  
angle has a mixed multiplicity. It has a multiplicity of 3 for the  
rotation around CA-CB bond axis, and a mulitiplicity of 1 with energy  
minimium at HA-CA-CB-OH equal to 0 degree. To this kind of dihedral, I  
don't know how to build a mixed muliplicity dihedral angle potential.

Best,
Lishan

> Hi Lishan,
>
> Your mail would be a bit more readable with more structure...
>
> Anyway, it says in the manual you can't do perturbation on the
> multiplicity. That makes sense, because interpolation from 1 to 3
goes
> through a whole series of rational numbers, but you can't have
> non-integer periods... If you must, you first have to remove the
> dihedral, i.e. bring the amplitude to 0, and then raise again to the
> other function.
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 30, 2011 at 3:15 AM,  <yaolisha at msu.edu> wrote:
>> Dear Gromacs users: I use gromacs.4-5-3 to calculate the free
energy changes
>> for the GTG to GAG alchemy process, where charge annihilation is
performed
>> first followed by soft core VDW calculation. When doing the soft
core VDW
>> calculation, I see this error message ?Fatal error: [ file
gtg_vdw.top, line
>> 314 ]: Proper Dih. multiplicity can not be perturbed
1.000000!=3.000000?.
>> Line 314 has the following content ?17 16 18 24 9? The atoms with
VDW radius
>> and well depth changes include 20 CT 3 THR CG2 20 -0.0000 12.01 CTD
0.0
>> 12.01 ; qtot 0.0439 21 HC 3 THR HG21 21 0.0000 1.008 HCD 0.0 1.008;
qtot
>> 0.1081 22 HC 3 THR HG22 22 0.0000 1.008 HCD 0.0 1.008; qtot 0.1723
23 HC 3
>> THR HG23 23 0.0000 1.008 HCD 0.0 1.008; qtot 0.2365 24 OH 3 THR OG1
24
>> -0.0000 16 OHD 0.0 16 ; qtot -0.4396 25 HO 3 THR HG1 25 0.0000
1.008 HOD 0.0
>> 1.008; qtot -0.0294 Atom types CTD, HCD, OHD, HOD are defined in a
separate
>> file and included in the topology file. My question is how to solve
this
>> problem and a related question is whether the overall setup is
correct.
>> Best, Lishan