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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Received on Thu Jun 27 2019 - 07:30:02 PDT
