Bilash,
So here's a few things:
(1) I have run what you gave me (tleap -f amber.in, after changing absolute
paths) and get:
...
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: ./thr_man_tutorial_AMAN_c_H.ac
----- Source of ./thr_man_tutorial_AMAN_c_H.ac done
/usr/local/amber22/bin/teLeap: Fatal Error!
charge: Argument #1 is of type Double must be of type: [unit molecule
residue atom list]
Here are some suggestions for correcting this error:
Verify the type of an argument with the desc command.
Check for alternate argument names with the list command.
usage: charge <object>
Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
(2) You have charge zero for AMA, which upon looking at it, is missing a
hydrogen (or something) on C1, so that's not correct;
(3) Looking at OLT, you have charge zero in the .ac file but it is clearly
-1 when I look at the structure; and
(4) You didn't exactly do what I suggested - i.e., generate .prepi and
attendant .frcmod files from those - nor have you included a file
- thr_man_tutorial_no-H.pdb - referenced in amber.in.
Good luck,
Todd
On Tue, Jan 2, 2024 at 8:11 AM BILASH MAITY <523cy1001.nitrkl.ac.in> wrote:
> Respected Todd Minehardt ,
> I am really sorry for late reply, as I was having some health issue. I
> have used the syntaxes you suggested. But still I am getting the same
> error. I have attached all the files with this email. Please find the
> attachments.
>
> ------------------------------
> *From: *"Todd Minehardt" <todd.minehardt.gmail.com>
> *To: *"BILASH MAITY" <523cy1001.nitrkl.ac.in>, "amber" <amber.ambermd.org>
> *Sent: *Saturday, December 30, 2023 11:39:05 PM
> *Subject: *Re: [AMBER] Failed to genarate parameters in Tleap
>
> Bilash,
> Instead of using keyword source, try:
>
> loadamberparams frcmod_AMAN
> loadamberprep <whatever your .prepi file name is>
>
> as it appears that the parsing error might be due to it expecting one
> format and getting another. I can attest
> to it working as advertised for the past 25 years (others on this list can
> double that, including at least a few who
> actually wrote the code and don't just use it like I do) in this manner,
> so let's
> get those issues straightened out.
>
> Regardless, how did you prepare the .prepi and .frcmod files (commands,
> specifically) and please include the
> .frcmod, .prepi, and source (meaning, the file(s) you created those from,
> such as the PDB files) if you continue to
> have issues.
>
> Cheers,
>
> Todd
>
> On Fri, Dec 29, 2023 at 11:07 PM BILASH MAITY <523cy1001.nitrkl.ac.in>
> wrote:
>
>> Respected Todd Minehardt,
>> Thank you for your suggetion. I have made frcmod file, and also put the
>> residue names as AMA and COLT. but I am still getting erros. This is the
>> input file
>> source
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
>> source
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/oldff/leaprc.ff14SB
>> source
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.protein.ff14SB
>> source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff
>> source frcmod_AMAN
>> source frcmod_THR
>> list
>> glyprot =loadpdb thr_man_tutorial.pdb
>> bond glyprot.2.OG1 glyprot.1.C1
>> savepdb glyprot man_thr_corr_amber_tutorial.pdb
>> saveamberparm glyprot man_thr-tutorial.top man_thr-tutorial.crd
>> quit
>>
>> This is the error I am getting now,
>>
>> ----- Source:
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff
>> ----- Source of
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff done
>> Log file: ./leap.log
>> Loading parameters:
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/parm/gaff.dat
>> Reading title:
>> AMBER General Force Field for organic molecules (Version 1.81, May 2017)
>> ----- Source: ./frcmod_AMAN
>> ----- Source of ./frcmod_AMAN done
>>
>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Fatal Error!
>> Error from the parser: syntax error
>>
>> Exiting LEaP: Errors = 1; Warnings = 0; Notes = 1.
>>
>> Thanking you,
>> Bilash Maity
>>
>>
>> ------------------------------
>> *From: *"Todd Minehardt" <todd.minehardt.gmail.com>
>> *To: *"BILASH MAITY" <523cy1001.nitrkl.ac.in>, "amber" <amber.ambermd.org
>> >
>> *Sent: *Friday, December 29, 2023 9:10:16 PM
>> *Subject: *Re: [AMBER] Failed to genarate parameters in Tleap
>>
>> Bilash,
>> You need to prepare and load .prepi/.frcmod files for residues AMA and
>> COLT - at least - since they are not part of the force fields you have
>> sourced.
>>
>> The non-integral charge is another matter, as some slop is
>> expected/common but I'd rather see -1.0XXX than -1.194; this could be an
>> artifact from not
>> having proper atom types/charges as mentioned above, or some other issue.
>>
>> I suggest stepwise debugging: get the modifications for AMA and COLT
>> prepared/loaded/okayed and go from there.
>>
>> Cheers,
>>
>> Todd
>>
>> On Fri, Dec 29, 2023 at 8:59 AM BILASH MAITY via AMBER <amber.ambermd.org>
>> wrote:
>>
>>> Respected Amber community,
>>> I am trying to make a bond between Threonine and Mannose using Tleap.
>>> Here is my input file,
>>>
>>> source
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
>>> source
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/oldff/leaprc.ff14SB
>>> source
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.protein.ff14SB
>>> source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff
>>> list
>>> glyprot =loadpdb thr_man_tutorial.pdb
>>> bond glyprot.2.OG1 glyprot.1.C1
>>> savepdb glyprot man_thr_corr_amber.pdb
>>> saveamberparm glyprot man_thr-tutorial.top man_thr-tutorial.crd
>>> quit
>>>
>>> This is the error I am getting:
>>>
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
>>> Converting C-terminal residue name to PDB format: COLT -> OLT
>>> Checking Unit.
>>>
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
>>> There is a bond of 6.323369 angstroms between:
>>>
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
>>> The unperturbed charge of the unit (-1.194000) is not integral.
>>>
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
>>> The unperturbed charge of the unit (-1.194000) is not zero.
>>> FATAL: Atom .R<AMA 1>.A<C1 1> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H1 2> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<C5 3> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H5 4> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<O5 5> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<C2 6> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H2 7> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<O2 8> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<HO2 9> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<C3 10> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H3 11> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<O3 12> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<HO3 13> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<C4 14> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H4 15> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<O4 16> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<HO4 17> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<C6 18> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H61 19> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<H62 20> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<O6 21> does not have a type.
>>> FATAL: Atom .R<AMA 1>.A<HO6 22> does not have a type.
>>> FATAL: Atom .R<COLT 2>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<COLT 2>.A<HG1 16> does not have a type.
>>> FATAL: Atom .R<COLT 2>.A<OT1 17> does not have a type.
>>> FATAL: Atom .R<COLT 2>.A<OT2 18> does not have a type.
>>>
>>> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Fatal Error!
>>> Failed to generate parameters
>>>
>>> Exiting LEaP: Errors = 1; Warnings = 6; Notes = 1.
>>>
>>> If any one can suggest the solution that wil be very helpful.
>>>
>>> Thanking You,
>>> BILASH MAITY
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
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Received on Tue Jan 02 2024 - 08:00:02 PST
