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 Tue Aug 25 2020 - 10:30:02 PDT
