Dear Ayesha,
Look at your leap.log file. You basically shouldn’t get errors. When there is an error, it means the program didn’t read in your file correctly. So you need to look at how you made the file and what part of it is not being recognized.
Maria
> On Aug 27, 2020, at 8:55 PM, Ayesha Fatima <ayeshafatima.69.gmail.com> wrote:
>
> Dear Maria,
> Thank you for the reply.
> Actually i did load my mol2 file before the frcmod and .lib files before
> the pdb complex file. But it was not recognised also.
> I used the command
> Tleap - f leaprc.protein.ff14SB
> Source leaprc.gaff
> lig = loadmol2 lig.mol2
> loadamberparams lig.frcmod
> Loadoff lig.lib
> Complex =loadpdb complex.pdb
>
> Is it the correct command?
>
> Thank you again
> Regards
> Ayesha
>
>
> On Fri, 28 Aug 2020, 7:02 am Maria Nagan, <maria.c.nagan.gmail.com> wrote:
>
>> For some reason I didn’t see your original post with the files.
>>
>> Did you load your ccl2_fragH.mol2 file into leap before you added your pdb
>> file?
>> Did you rename your ccl2_fragH.mol2 residue name PCA in your mol2 file?
>>
>> You’re right your new non-standard residue is not being recognized. Every
>> non-standard residue needs to have a .lib file (or mol2 file) and an frcmod
>> file loaded. If you look at some of the leaprc files available, you will
>> see that they always load in an lib file and then the frcmod file. You have
>> to tell leap the you have a new residue named PCA with certain atom types.
>> Then you need to load in an frcmod file that tells leap that your new PCA
>> residue has parameters.
>>
>> --Maria
>>
>>> On Aug 27, 2020, at 6:42 PM, Ayesha Fatima <ayeshafatima.69.gmail.com>
>> wrote:
>>>
>>> Good morning everyone.
>>> I am having the same problem. I posted my question but it is waiting
>>> approval to be posted as i wrote it too long, pethaps.
>>> Thank you
>>> Regards
>>>
>>> On Fri, 28 Aug 2020, 3:56 am Erika Davidoff, <erikadavidoff.gmail.com>
>>> wrote:
>>>
>>>> Dear Amber users,
>>>>
>>>> I am new to computational modeling and have an issue I've been trying to
>>>> solve. I am working with a PDB of a protein that has mostly standard
>>>> residues and one non-standard HETATM called PCA that contains 8 atoms.
>> To
>>>> get the parameters for this non-standard residue, I made a separate PDB
>>>> with the one residue, added hydrogens to it and used antechamber to
>>>> generate a mol2 file:
>>>>
>>>> antechamber -i ccl2_fragH.pdb -fi pdb -o ccl2_fragH.mol2 -fo mol2 -at
>> amber
>>>> -c bcc
>>>>
>>>>
>>>> Then I used parmchk2 to generate a modified force field parameters file
>>>> that has a lot of parameters:
>>>>
>>>> parmchk2 -i ccl2_fragH.mol2 -f mol2 -o ccl2.frcmod
>>>>
>>>>
>>>> Then I have a tleap script that includes the lines
>>>>
>>>> loadamberparams ccl2.frcmod
>>>>
>>>> ccl2 = loadPdb ccl2.pdb
>>>>
>>>>
>>>> and proceeds to add a peptide to the system and solvate it. When I run
>>>> this, I get errors for all eight atoms in the non-standard residue:
>>>>
>>>> Unknown residue: PCA number: 0 type: Terminal/beginning
>>>>
>>>> ..relaxing end constraints to try for a dbase match
>>>>
>>>> -no luck
>>>>
>>>> Creating new UNIT for residue: PCA sequence: 1
>>>>
>>>> Created a new atom named: N within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: CA within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: CB within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: CG within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: CD within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: OE within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: C within residue: .R<PCA 1>
>>>>
>>>> Created a new atom named: O within residue: .R<PCA 1>
>>>>
>>>> ...
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<O 8> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<C 7> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<OE 6> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<CD 5> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<CG 4> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<CB 3> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<CA 2> does not have a type.
>>>>
>>>> FATAL: Atom .R<PCA 9>.A<N 1> does not have a type.
>>>>
>>>>
>>>> I have attached: ccl2.pdb, the original protein file (straight from the
>>>> database); ccl2_fragH.pdb, the file with the one residue; ccl2.frcmod;
>> and
>>>> my tleap script.
>>>>
>>>> Thank you for your help!
>>>>
>>>> Best,
>>>> Erika
>>>>
>>>> *Erika J. Davidoff *
>>>> *Rutgers University*
>>>> Department of Biomedical Engineering
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>>>>
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Received on Thu Aug 27 2020 - 18:00:03 PDT
