Dear Alessandro,
The command "loadamberprep" has to be applied before loading the PDB structure...
Have you renamed the whole molecule in "file.pdb" to match "res.in"? Remember antechamber deals with single units, it won't return separated topologies for composing residues (e.g. DA, DG, DT, DC), then you lost the by-residue identity of the DNA and the building block capability...
As you are facing no error when generating the toplogy, my guess is you aren't using the "res.in" parameters at all, but the cmd file leaprc.ff19SB, which includes the force field "parmbsc0" for each residue in the DNA...
Let me insist on this issue... why modeling the DNA by GAFF parameters?
Best,
Matias
------------------------------------
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: "Alessandro LANDI" <alelandi1.unisa.it>
Para: "David Case" <david.case.rutgers.edu>, "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 27 de Junio 2019 11:24:24
Asunto: Re: [AMBER] Problem with mol2 file generated by Antechamber
Dear prof. Case and all,
I am using AmberTools 1.4. I thank you very much for your suggestion, and I
tried removing sodium atoms. In this way the LeaP computations end fine.
However, I still got some warnings in the frcmod file (attached), and
moreover the subsequent Sander minimization eventually fails (I got the
following error: "REPEATED LINMIN FAILURE").
I have tried to fix this error in several ways, and I may have found a
solution, as reported at the link
http://signe.teokem.lu.se/~ulf/Methods/resp.html
However, to follow that procedure, I need to read from two separate files
the geometry and the charges in LeaP. I have tried to do so by resorting to
"loadamberprep" command in LeaP.
The step-by-step methodology I have followed is:
1) Generating the DNA sequence using 3DNA (In this way I have the file
"file.pdb")
2) Converting the PDB file and performing a Gaussian calculation, using the
standard command line
#p HF/6-31G* Pop=MK IOp(6/33=2,6/41=10,6/42=17)
(In this way I have the file "g09.out")
3) Converting the Gaussian output (file g09.out) to prep format with
Antechamber, using the command line
antechamber -fi gout -fo prepi -c resp -i g09.out -o res.in -rn RES
-at amber -pf y
4) Loading the geometry from the pdb file and the charges from prep file in
LeaP, using the following lines in the input file "leap.in"
source leaprc.ff99SB
dna = loadpdb file.pdb
loadamberprep res.in
saveamberparm dna chrg.prmtop chrg.inpcrd
quit
5) Performing the Sander minimization step, using the following line in the
input file:
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 50,
ntb = 0,
igb = 1,
cut = 16.0,
&end /
The computations end fine, but I noticed that in the "chrg.prmtop" file I
get the same charges either including the command "loadamberprep res.in" in
the file "leap.in" or not. So I think I am doing something wrong.
Thus my question is: is it actually possible in LeaP to read the geometry
and the charges from two separate files? How should I operate?
Any help would be appreciated.
Thanks a lot,
Alessandro
Il giorno sab 15 giu 2019 alle ore 14:54 David Case <david.case.rutgers.edu>
ha scritto:
> On Thu, Jun 13, 2019, Alessandro LANDI wrote:
> >
> >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
>
> What version of AmberTools are you using. Recent versions should(?)
> complain that antchamber is for organic molecules only, and doesn't
> handle Na+ ions. The RESP charges for standard nucleotides were
> generated from anions, not constructs neutralize with Na+, so that
> might be the best way to proceed.
>
> >
> >"Na 0.000 0.000 ATTN, need revision"
> >"h5-na-cc-nd 1.1 180.0 2.0 Using default
> >value"
>
> Clearly antechamber has gone wrong here, thinking that sodium has
> chemical bonds to other atoms. So, try removing your sodium ions.
>
> ...good luck...dac
>
>
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>
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Received on Thu Jun 27 2019 - 08:30:03 PDT
