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
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Dec 30 2023 - 10:30:02 PST
