[gmx-users] Re: Re: Re: help with a chromophore of GFP
Mark Abraham
mark.j.abraham at gmail.com
Wed Apr 10 11:30:05 CEST 2013
On Wed, Apr 10, 2013 at 8:49 AM, Anna Marabotti <amarabotti at unisa.it> wrote:
> 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 three lines that I understand you have introduced are not needed.
CT-CT-N-C and C-N-CT-CT are the same interaction, and later when grompp
looks up the parameters for a [dihedral] from the [dihedraltypes] it looks
for either.
> ..............................**...
>
> 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?
>
The error message looks wrong. It was introduced at about the same time as
dihedraltype 9, but the history of that part of code development is very
murky, and much was not well documented at the time. Even professors are
human! I suspect that a subsequent change has broken something that worked
well at the time, and because the original purpose was unclear and there
were no test cases for the code, nobody knew there was a problem (if one
actually exists!). Still, it doesn't matter for your case, because you
don't need the duplicate [dihedraltypes] at all.
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?
>
Type 9 is a proper dihedral, per the tables of chapter 5. Presumably you
have an entry in an [impropers] section whose atoms match that type. One or
other entry needs to move section or change type to get a match.
> 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?
>
As above, a dihedral interaction is defined over an ordered set of 4 atoms,
but reversing the order describes the same interaction. grompp doesn't
bother with any aesthetics here; even if it wanted to, and if the .rtp
entry and the [dihedrals]/[impropers] section were in the opposite sense,
there's no clearly correct "orientation" to use. Similarly for interaction
ordering. The one-to-one mapping in the lookup is important, and nothing
else is.
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).
Seems sensible, but do be aware that Antechamber has optimized the other
parameters for a context other than that in which you plan to use them.
Whether that is significant is difficult to show. What is easy to do (and I
think I have said this before in this thread) is to check the docs to see
if you can do the original Antechamber calc in the constrained context. If
not, do hassle the Antechamber developers to document/implement how to do
it! You're not the only one who would want this functionality.
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?
>
The warnings here pertain to possible violations of the assumptions by
which grompp tries to look up parameters for intractions in your
[moleculetype]. The errors occur when grompp cannot do that look-up.
Omitting what looks like a duplicate would lead to an error if you aren't
as picky as the computer program has to be in doing the look up. I think
your procedure looks fine, except for the proper/improper mismatch above.
Mark
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)
>
> --
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