[gmx-users] Re: help with chromophore of a GFP

[Anna Marabotti]

Dear gmx-users, dear Mark,
thank you for all the help you are giving me for this subject. I'm still 
proceeding to my target..
Thanks to your previous suggestions, I was able to parametrize bonds and 
angles of CFY. Now I'm dealing with dihedrals...

In the parameter files derived by Antechamber I have 2 different 
sections for dihedrals and impropers. They are characterized by these 
values:

DIHEDRALS:
The actual torsion potential is (PK/IDIVF)* (1 + cos(PN*phi - PHASE). 
The components should be those reported in the column of the file, i.e.:

- first column: IDIVF: a factor by which the torsional barrier is divided
- second column: PK: the barrier height divided by a factor of 2
- third column: PHASE: the phase shift angle in torsional function (in deg)
- fourth column: PN: the periodicity of the torsional barrier

An example for this section is:

DIHE

NT-CT-C -O10.000180.0002.000same as X -c -c3-X

NT-CT-C -N10.000180.0002.000same as X -c -c3-X

NT-CT-CT-CT10.1560.0003.000same as X -c3-c3-X

NT-CT-CT-HC10.1560.0003.000same as X -c3-c3-X

CT-C -N -CT12.500180.0002.000same as X -c -n -X
................................


IMPROPERS:
The input is the same as for dihedrals except that the torsional barrier 
height is NOT divided by IDIVF. Therefore the components are:

- first column: PK: the barrier height divided by a factor of 2
- second column: PHASE: the phase shift angle in torsional function (deg)
- third column: PN: the periodicity of the torsional barrier
An example is:

IMPROPER

CT-N -C -O1.1180.02.0Using default value

C -CT-N -H1.1180.02.0Using default value

CK-CT-CM-NB1.1180.02.0Using default value

C -CC-CC-NB1.1180.02.0Using default value

..........................

I should report these information in ffbonded.itp in order to fix the 
values for dihedrals for CFY. However, I have some difficulties in doing 
it, and description in Table 5.5 of the manual is rather cryptic to me. 
First of all, I don't understand why in ffbonded.itp there are two 
separated [dihedral types] sections, I see that in the first section the 
column that I presume corresponds to "f.tp" in Table 5.5 (but in 
ffbonded.itp it is called "func"), is all equal to 4, whereas in the 
second section this value is 9 for all.

An example for the fist section is:
[ dihedraltypes ]
;i  j   k  l     func      phase      kd      pn
CA  CA  CA  OH       4      180.00     4.60240     2     ; new99
H5  O   C   OH       4      180.00     4.60240     2     ; new99
H5  O   C   OS       4      180.00     4.60240     2     ; new99
CM  CT  CM  HA       4      180.00     4.60240     2     ; new99
CA  CA  CA  Br       4      180.00     4.60240     2     ; new99
.................................

and for the second section:

[ dihedraltypes ]
;i   j   k   l       func
  CT  CT  OS  CT    9       0.0      1.60247     3  ;
  CT  CT  OS  CT    9     180.0      0.41840     2  ;
  C   N   CT  C     9       0.0      1.12968     2  ; new for 99sb
  C   N   CT  C     9       0.0      1.75728     3  ; new for 99sb
  N   CT  C   N     9     180.0      1.88280     1  ; new for 99sb

If I understand correctly, then this means that the first section is for 
periodic improper dihedrals, and the second section is for proper 
dihedral multi, right? I don't understand the difference between 
"improper dih." f.tp. 2 and "periodic improper dih." f.tp.4. Moreover, 
if I can imagine that PHASE and PN mean the same in both cases 
(ffbonded.itp and Antechamber values), I don't understand if kd is 
corresponding to PK, or to the result of (PK/IDIVF)* (1 + cos(PN*phi - 
PHASE).

Could you please give me some hints on how I can edit correctly the 
ffbonded.itp file using data obtained by Antechamber?

Thanks again and best regards
Anna