Hi,
1. Clarification on my previous comments:
Prior to AmberTools 17 antechamber silently failed to read charges
from a nonconforming -cf file and used charges that may have already
been read from the main input file -i. The patch below for charge.c
will get AmberTools 20 back to that dubious behavior.
2. What is the intended antechamber protocol ?
As you correctly indicate, -c rc requires -rf file, else the error
you show below will be produced.
I have asked the antechamber authors this question, see issue 155.
Presently the workaround is this rather silly approach:
antechamber -fi mol2 -i m.mol2 -c wc -cf m.chrg -fo foo -o bar
antechamber -fi mol2 -i m.mol2 -c rc -cf m.chrg ...
scott
On Tue, Aug 25, 2020 at 07:07:48PM +0200, Marek Maly wrote:
> Hi Scott,
>
> first of all thank you for prompt reaction !
>
> Dne Sat, 22 Aug 2020 00:02:13 +0200 Scott Brozell
> <sbrozell.iqb.rutgers.edu> napsal/-a:
>
> > 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
> > )
>
> OK, so parameter -cf is possible to use just for file containing ONLY
> charges.
>
> I just notice again that up to the AmberTools16 (including this version)
> this was never problem and my script worked perfectly with "-cf input mol2
> file".
>
> If I now (in AmberTools19) delete from my scrit problematic "-cf input
> mol2 file" (and use "-dr no" to prevent errs thanks to presence of "Si"
> atom) it writes:
>
> Info: Finished reading file (Mol_m1-o1-sm.mol2); atoms read (180), bonds
> read (180).
> Running: /opt/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /opt/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> /opt/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Cannot open file () with mode (r).
> No such file or directory
>
>
> So which are the right Antechamber parameters/(parameters arguments) usage
> in actual AT version to simply create output mol2 file with GAFF atom
> types from the mol2 input file, which already contains RESP charges (just
> proper atom types are missing) ?
>
> Best wishes,
>
> Marek
>
>
>
> >
> > 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.
> >>
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Received on Thu Aug 27 2020 - 15:00:02 PDT
