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

[Anna Marabotti]

Dear gmx-users, dear Mark,
the soap-opera is going on... and I am so sorry to bother you again and
again (but I hope that this will be of help for future people that will
have the same problem...).

Summary of the last episode: I found a way to convert the parameters of
dihedrals and impropers calculated with Antechamber to Gromacs format,
and I added these values in ffbonded.itp. Now my ffbonded.itp is
complete, so I launched grompp on the protein structure with the
chromophore (I already did pdb2gmx, editconf and genbox with no
problems), and these are the warnings and the errors I obtained:

grompp_d -f em.mdp -c prot_boxwat.pdb -o prot.tpr -p topol.top


WARNING 1 [file ffbonded.itp, line 464]:

   Overriding Proper Dih. parameters.

   Use dihedraltype 4 to allow several multiplicity terms.

   old: 0 8.368 1 0 8.368 1

   new: C   N   CT  CT    9       0.0      8.36800     2



WARNING 2 [file ffbonded.itp, line 465]:

   Overriding Proper Dih. parameters.

   Use dihedraltype 4 to allow several multiplicity terms.

   old: 0 8.368 2 0 8.368 2

   new: C   N   CT  CT    9       0.0      1.67360     3


[other warnings similar to this one, the last warning is:]


WARNING 6 [file ffbonded.itp, line 570]:

   Overriding Proper Dih. parameters.

   Use dihedraltype 4 to allow several multiplicity terms.

   old: 0 0 3 0 0 3

   new: H1  CT  CT  OH    9       0.0      1.04600     1


Generated 2211 of the 2211 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 2211 of the 2211 1-4 parameter combinations



ERROR 1 [file topol.top, line 31084]:

   No default Improper Dih. types


[other 16 error messages similar to these ones]


1) Concerning warnings.
What I understand in the warning is that I defined some values in a
wrong way.
In order to understand what was wrong, I looked both at ffbonded.itp and
to my topol.top file.

In the ffbonded.itp file, all warning messages but one (the last one)
are referred to some definitions that I added to the file. For example,
in the ffbonded.itp file, I see the definitions for dihedral CT-CT-N-C,
that are the followings:

...............
CT  CT  N   C     9       0.0      8.36800     1  ; new for 99sb
  CT  CT  N   C     9       0.0      8.36800     2  ; new for 99sb
  CT  CT  N   C     9       0.0      1.67360     3  ; new for 99sb
.................................

Since in the Antechamber parameters I found paramteres for dihedral
C-N-CT-CT, I decided to add them to the file, in this way:
...............
CT  CT  N   C     9       0.0      8.36800     1  ; new for 99sb
  CT  CT  N   C     9       0.0      8.36800     2  ; new for 99sb
  CT  CT  N   C     9       0.0      1.67360     3  ; new for 99sb
C   N   CT  CT    9       0.0      8.36800     1  ; REF. CT-CT-N-C, SET
MANUALLY FOR CFY, DIFFERENT FROM ANTECHAMBER (GAFF PAR.)
  C   N   CT  CT    9       0.0      8.36800     2  ; REF. CT-CT-N-C,
SET MANUALLY FOR CFY, DIFFERENT FROM ANTECHAMBER (GAFF PAR.)
  C   N   CT  CT    9       0.0      1.67360     3  ; REF. CT-CT-N-C,
SET MANUALLY FOR CFY, DIFFERENT FROM ANTECHAMBER (GAFF PAR.)
.................................

The warning message is referred to the second and third parameter I
added; the first one (marked with "1") is not cited.
My question is: how to deal with the warning message saying that I am
"overriding Proper Dih. parameters" and that I should "Use dihedraltype
4 to allow several multiplicity terms." Do I have to add all 3
parameters into section "4" instead of "9"? Do I have to remove all the
three parameters? or only the last two? why the three default parameters
described just before mine are present as multiple in this section and
not in section "4"? Moreover, If I understand correctly info in Table
5.5, dihedraltype 4 should be assigned to "periodic improper dih.", but
these are not improper dihedral types! How to deal with this problem?

Second question: the last warning message is referred to a parameter
that is already present in the default ffbonded.itp file. It is defined
in this way:
H1  CT  CT  OH    9       0.0      1.04600     1  ; Junmei et al, 1999
there are no other definitions for this dihedral in this file, and I did
not add any information about this dihedral (or at least, I did not do
it intentionally). Why this warning?

2) Concerning the errors.
I understand that Gromacs does not find correct definitions for
dihedrals of my chromophore.
I don't understand if this comes from the definition of dihedrals that I
included in aminoacids.rtp or from the parameters that I included in
ffbonded.itp.

In aminoacids.rtp I added the section [impropers] just below the section
[bonds]. Impropers are defined like that, using the atom names (that are
the same as in the .pdb file that I grompp'ed):
  [ impropers ]
     -C   CA1     N   H04
    CA4    +N     C     O
     C2   CB2     N   CA2
................................................
    CZ1   CD2   H14   CE2
    CE2   CG1   H10   CD2
When I looked at the lines in topol.top cited in the error message, I
found that for several impropers, the definition was the opposite with
respect to the one that I included in aminoacids.rtp. For example, in
topol.top the atoms composing the last improper of aminoacids.rtp
(CE2-CG1-H10-CD2) are indicated exactly in the opposite order
(CD2-H10-CG1-CE2). Instead, in other impropers, atoms are reported
exactly in the same order in both files. Moreover, the order in which
impropers are present in the aminoacids.rtp file is not the same that I
find in topol.top (eg. the last improper CE2-CG1-H10-CD2 in
aminoacids.rtp is not the last improper in topol.top). Do these two
differences matter for the correct recognition of dihedrals?

Second question: I decided not to implement all improper parameters
calculated with Antechamber on my molecule. In fact, they were
calculated using GAFF instead of Amber99sb FF (the two ff are fully
compatible, but since some of these parameters are referred to moieties
of the chromophore that are easily recognizable as former amino acid
residues, I prefer to use the classical Amber99sb parameters for these
residues). Therefore, I did not add for some of these impropers the
specific parameters, preferring to use the general ones already defined
in ffbonded.itp. Can this fact contribute for this error?

I hope that all is clear; always many thanks for your help, 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 at 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)