On Thu, Jun 27, 2019 at 10:26 AM Alessandro LANDI <alelandi1.unisa.it> wrote:
>
> Dear prof. Case and all,
> I am using AmberTools 1.4. I thank you very much for your suggestion, and I
Yikes! That version is coming up on 10 years old! I *highly* recommend
you update to the most recent version (AmberTools 19:
http://ambermd.org/GetAmber.php).
-Dan
> 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 - 08:30:05 PDT
