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 - 09:00:03 PDT
