Suchetana,
you attached a leap file different from the input you provided in your
e-mail.
Maybe the residue numbering is still the problem.
I'd recommend to
- run your leap input without the bond command
- note down the residue numbers of the cyclic peptide terminal residues
from the resulting pdb file
- add debug output lines like "desc cplx.NNN" and "desc cplx.MMMM" with
NNN and MMM being the residue numbers of the cyclic peptide to your leap
script
- include the bond command and run leap again.
Personally, I'd also rename the HETATM cards into ATOM, since all the
residues are known to Amber (you have some HETATM entries for normal
amino acids in your cyclic peptide).
Maybe this helps.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 28.11.2022 um 22:41 schrieb Suchetana Gupta via AMBER:
> As Carlos mentioned, I rechecked the residue numbers and put them as per
> how it is in the input PDB file. Everything seems to be correct.
> To give a perspective:
> The input PDB file starts from 442, goes on to 798. Then there is a Zn at
> 801 and then a cyclic peptide from 1 to 8.
> Attaching the input PDB file and leap input file for reference.
>
> I'd appreciate any help.
>
> Thanks!
> Suchetana
>
> On Mon, Nov 28, 2022 at 1:36 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> wrote:
>
>> Have you checked the atom names that are being connected through the bond
>> command. As you have mentioned that the residue numbers are correct, may be
>> there is some problem with the atom names. Otherwise it looks fine to me.
>>
>> Best,
>> Satyajit Khatua
>>
>> Get Outlook for Android <https://aka.ms/AAb9ysg>
>> ------------------------------
>> *From:* Suchetana Gupta via AMBER <amber.ambermd.org>
>> *Sent:* Tuesday, November 29, 2022 2:51:06 AM
>> *To:* David A Case <david.case.rutgers.edu>; AMBER Mailing List <
>> amber.ambermd.org>
>> *Subject:* Re: [AMBER] Simulating a Protein - cyclic peptide complex -
>> question
>>
>> Hello!
>> I tried following your suggestion first, David and used the following as my
>> leap input commands:
>>
>> source leaprc.protein.ff14SB
>> source leaprc.gaff
>> source leaprc.water.tip3p
>> loadoff atomic_ions.lib
>> loadamberparams frcmod.ionsjc_tip3p
>> loadamberparams frcmod.ions234lm_126_tip3p
>> loadamberparams SHA.frcmod
>> loadamberparams NLU.frcmod
>> loadAmberPrep SHA.relabeled.prepi
>> loadAmberPrep NLU.relabeled.prepi
>> cplx=loadPDB copy.pdb
>> bond cplx.355.N cplx.362.C
>> savepdb cplx des431_complex_out.pdb
>> saveAmberParm cplx des431_c.top des431_c.crd
>> quit
>>
>>
>> I got this error:
>> bond: Argument #1 is type String must be of type: [atom]
>>
>>
>> usage: bond <atom1> <atom2> [order]
>>
>>
>> I am pretty sure that the residue number is correct since I had used
>> savePDB option once and checked it, before using the bond command.
>>
>> Can you please help?
>>
>> Thanks
>> Suchetana
>>
>>
>>
>> On Fri, Nov 11, 2022 at 9:12 AM Suchetana Gupta <suchetana.gupta.gmail.com
>>>
>> wrote:
>>
>>> Dear David and Anselm
>>> I think I will try out both the suggestions once I figure out the
>> solution
>>> to my other question that is on a different mail thread: parameter
>>> generation for noncanonical residues. I will get back to you.
>>> just a quick question to Anselm, what is this combine command in tleap?
>>> Sorry, I could not find this and would really appreciate a help with the
>>> syntax. I am using Amber 20
>>> Thanks
>>> Suchetana
>>>
>>> On Fri, Nov 11, 2022 at 8:25 AM David A Case <david.case.rutgers.edu>
>>> wrote:
>>>
>>>> On Thu, Nov 10, 2022, Suchetana Gupta via AMBER wrote:
>>>>
>>>>> I am trying to simulate a protein-cyclic peptide complex and have a
>> basic
>>>>> question.
>>>>>
>>>>> My question is, when I simulate the peptide-protein complex, how do I
>>>> frame
>>>>> the leap input file? I am concerned about the loadPDB part.
>>>>
>>>> Here's what I always do. It's not necessarily the best way, but to me,
>> it
>>>> seems simplest.
>>>>
>>>> Make a single PDB file with both the protein and the peptide, separated
>>>> by a
>>>> TER card. Then in your leap.in file, load all necessary libraries and
>>>> frcmod files. Then use a single loadPdb file (not loadPdbusingseq) to
>>>> get a unit that has everything you want. Use the bond command to add
>> the
>>>> missing "cyclic" bond for the peptide. (Use the "desc" command first to
>>>> see
>>>> which residue numbers correspond to the peptide).
>>>>
>>>> Then you can continue with solvate commands, etc. If tleap reports an
>>>> error, try to see if you can fix it.
>>>>
>>>> To me (maybe not to others) it seems simpler to use a text editor to
>>>> create
>>>> a starting PDB file that has everything I want than to bother with
>> several
>>>> loadPdb commands and try to grok how combine these later inside tleap.
>>>>
>>>> ....good luck...dac
>>>>
>>>>
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Received on Tue Nov 29 2022 - 02:30:02 PST
