Dear Alessandro,
If it's just a matter of charges, then why don't you just modify the parameter of a well established DNA force field instead of building everything from scratch using the gaff ones?
For example... I think a better way may be to fork the parmbcs1 library to have a version of your own residues with the new charge distribution... That could be particularly useful if you then pretend to compare your results with and without ionization, in which case the only difference are the charges rather than other parameters... if the system still blows up, then you will know who should be blame for...
Just thoughts...
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: sribone.fcq.unc.edu.ar
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 13 de Junio 2019 12:35:38
Asunto: Re: [AMBER] Problem with mol2 file generated by Antechamber
I think that your problem is the atom type on your mol2 file format. You
should try the sybyl format on your mol2 file using the -at sybyl flag on
antechamber.
Good luck.
> Dear all,
> I have a problem concerning the use of MOL2 or PDB files generated by
> antechamber after a Gaussian ESP calculation. The system is B-DNA.
>
> After generating a pdb for a short DNA sequence (say GTG) with the
> 'fiber'
> command of 3DNA, I used Molden to convert it to xyz format and to add the
> missing hydrogens. Then I have added Na+ ions to achieve neutrality and
> finally I have performed a Gaussian09 calculation using the standard
> command line:
>
> #p HF/6-31G* Pop=MK IOp(6/33=2,6/41=10,6/42=17)
>
> I need a new set of RESP charges (rather than using the internally stored
> ones) because I need also to simulate ionized DNA sequences.
>
> After the Gaussian computation, The next step would be using Antechamber
> to
> get RESP charges and a MOL2 file having the same coordinates as the
> Gaussian09 output file.
>
> Let the G09 output be 'g09.out' and the mol2 files be 'file.mol2'. Of
> course, the latter should be compilant with "tleap" and should allow
for
> the addition of a solvent box (e.g. by using "solvateoct TIP3P"). I
used
> the following command lines:
>
> antechamber -i g09.out -fi gout -o file.mol2 -fo mol2 -c resp -s 2
> parmchk -i file.mol2 -f mol2 -o file.frcmod
>
> That step ends fine. However, in the file "file.frcmod" (attached)
several
> problems are reported, among which:
>
> "Na 0.000 0.000 ATTN, need revision"
> "h5-na-cc-nd 1.1 180.0 2.0
Using default
> value"
>
> Then I use leap, with solvateoct and TIP3P and it ends up normally.
> However, when I try to run an initial Sander minimization. just to
relax
> the solvent molecules of the box, I get a "Segmentation Fault" error.
> Indeed, the sander output shows that after a few cycles the RMSD goes to
> very large values.
>
> As a newbie I may be wrong, but it seems to me that the problem
originates
> from the conversion from Gaussian09 to mol2 format. I also tried a
> conversion to PDB instead of using MOL2, but the same failure occurs.
>
> How can I check that antechamber has correctly assigned the atom type
(see
> file.mol2 attached) to all atoms? It is very strange, because all the
> atom
> types sholud be included in the standard AMBER force field, as I am faced
> with DNA.
>
> What am I doing wrong? How should I process the files from
> Gaussian/Antechamber in order to have proper files for sander to carry
out
> minimization, equilibration, dynamics and so on?
>
> Any help would be appreciated.
>
> Thanks a lot,
> Alessandro
>
>
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Received on Thu Jun 13 2019 - 09:30:01 PDT
