Hi,
A mol2 file is not a valid format for -cf.
(-cf rc expects only charges; see the result of -cf wc for an example, eg:
-0.174900 0.149300 0.272000 -0.174900 0.149300 -0.131900 0.132800 -0.056100
)
However, prior to the enhanced error reporting in AmberTools 17
antechamber silently failed to read charges from the -rf file and
used charges that may have already been read from the main input file -i.
Here's a workaround that gets back to that behavior while we work
on an improved approach.
*** 20.c 2020-04-27 21:19:42.000000000 -0400
--- 20m.c 2020-08-21 17:53:52.451689802 -0400
*************** void rcharge(char *filename, int atomnum
*** 372,379 ****
}
fclose(fpcharge);
if (number == 0) {
! eprintf("Unable to find charges in file (%s).\n"
! "Verify the filename and the file contents.", filename);
}
// if ((*minfo).usercharge < -9990.)
if ((*minfo).icharge < -9990.)
--- 372,379 ----
}
fclose(fpcharge);
if (number == 0) {
! printf("\nUnable to read charges in the -cf file (%s).\n"
! "Using charges from the -i input file.", filename);
}
// if ((*minfo).usercharge < -9990.)
if ((*minfo).icharge < -9990.)
scott
On Thu, Aug 20, 2020 at 09:02:00PM -0400, Scott Brozell wrote:
> Hi,
>
> Marek, thanks for the detailed bug report.
> I have reproduced the problem and will start debugging.
>
> scott
>
> ps
> why did the chicken cross the road ?
> it was amberlating !
>
> On Thu, Aug 20, 2020 at 12:21:08PM +0200, Marek Maly wrote:
> >
> > I would like to draw attention to a problem regarding the specific use of
> > the antechamber and parmchk / parmchk2 programs, starting with the
> > AmberTools17 version. It is the use of these routines to create mol2 and
> > frcmod outputs from the mol2 input, where the only operation required is to
> > add gaff atom types to the mol2 output file and eventually to create also
> > the appropriate frcmod file. The input mol2 file is in my case obtained as
> > the output from R.E.D. IV program, used for calculation of partial charges
> > using RESP method. At first I thought that the problem with this relatively
> > simple action, which the antechamber and parmchk programs handled easily
> > until version 16, is due to the presence of the foreign chemical element
> > "Si" (atom no. 80) in my residues, but as it turned out (after the Si -
> > substitution Si - > C in the input mol2 file) this problem is more general
> > in nature. Unfortunately, the problem persists even after this substitution
> > and even after disabling the acdoctor routine (running antechamber with "-dr
> > no") and possibly "freezing" non-standard bonds in the input mol2 file with
> > "f". In the best (AT19) case, all key Amber files are created:
> >
> > ANTECHAMBER_AC.AC
> > ANTECHAMBER_AC.AC0
> > ANTECHAMBER_BOND_TYPE.AC
> > ANTECHAMBER_BOND_TYPE.AC0
> > ATOMTYPE.INF
> >
> > which are moreover identical (except for the letter "f" for frozen bonds) to
> > the same files produced by AmberTools16.
> >
> > However, my calculation script in AmberTools19 case still ends with an
> > absurd error:
> >
> > "Unable to find charges in file (Mol_m1-o1-sm.mol2)"
> >
> > where Mol_m1-o1-sm.mol2 is the input mol2 file. This is of course nonsense,
> > considering the existence of all the Amber files mentioned above. So in
> > spite the perfect creation of all *.AC, *.AC0 and INF files neither the
> > output mol2 file nor the frcmod file is created.
> >
> > I would be very grateful for advice on how to get such great output with
> > AmberTools19 or later (mol2 file with added atom types and possibly frcmod
> > file - it is clear to me that in the case of a foreign chemical element, the
> > frcmod file will not contain concrete bond / nonbond values parameters) as
> > could be obtained using antechamber and parmchk in AmberTools16 and older
> > versions. This functionality is key for my work and I hope there exists a
> > more elegant solution than maintaining an alternative old version of
> > AmberTools16 just for this specific need.
> >
> > The inputs and outputs for one specific residue are available in the
> > attached file, namely:
> >
> > #1 AmberTools16
> > a) using parmchk
> > b) using parmchk2
> > There are identical mol2 outputs but different frcmod outputs (in case b) is
> > this file empty)
> >
> > #2 AmberTools19
> > a) using parmchk2 (without modifying the input mol2 script and without
> > adding the "-dr no" parameter to the antechamer command)
> >
> > b) using parmchk2 (unusual "Si-x" bonds are frozen with "f" and the
> > antechamber is started with the parameter "-dr no")
> >
> > You may easily try/check also the case, were the "Si" atom (number 80) is
> > substituted with "C" atom, and "-dr no" + "f" are eventually used.
> >
> > FILES
> >
> > input mol2 file: Mol_m1-o1-sm.mol2
> > calculation script: MakePREPandCHECK_MOL2_TO_MOL2.sh
> > output mol2 file: Mol_m1-o1-sm_withAT.mol2 (created just in AT16 case)
> > output frcmod file: Mol_m1-o1-sm.frcmod (created just in AT16 case, please
> > notice the difference between parmchk ans parmchk2 case).
> >
> > Then there are the usual Amber outputs and StdOut and ErrOut files
> > (SCREEN_OUTPUT_ATxy.txt, ERR_ATxy.txt) with informations/errs reported by
> > antechamber/parmchk/2 programs on the screen.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Csbrozell%40iqb.rutgers.edu%7C79fd0a0262c74348fa6f08d8456deff6%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637335685762534406&sdata=JJPbVaxdBw17nf9HGGSPSiYr6jQMvfVvBH%2Foc%2FUIIBU%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 21 2020 - 15:30:02 PDT
