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 - 08:00:06 PDT
