Dear Amber users,
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. If I understand correctly, the components of the torsional potential are those reported in the column of the file, i.e.:
DIHEDRALS:
- 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-O 10.000 180.000 2.000 same as X -c -c3-X
NT-CT-C-N 10.000 180.000 2.000 same as X -c -c3-X
NT-CT-CT-CT 10.156 0.000 3.000 same as X -c3-c3-X
................................
IMPROPERS:
- 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-O 1.1 180.0 2.0 Using default value
C -CT-N-H 1.1 180.0 2.0 Using 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, since the values that are reported in that file are:
[ dihedraltypes ]
;i j k l func phase kd pn
CA CA CA OH 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
.................................
where I assume that "phase" and "pn" are the same as PHASE and PN in Antechamber file, "func" is the descriptor of the type of dihedral (e.g. in this case 4 stands for "periodic improper dihedral", and 9 for "proper dihedral multi"), but I don't find a correspondence for kd in the Antechamber parameters. In ffbonded.itp file, kd is expressed in kJ/mol. Moreover, I am not sure that "periodic improper dihedral" is the same type of dihedral angle than IMPROPER is and "proper dihedral multi" is the same type of dihedral angle than DIHE is.
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
--
______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti.unisa.it
Skype: annam1972
"When a man with a gun meets a man with a pen, the man with the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)
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Received on Thu Apr 04 2013 - 03:30:03 PDT
