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 Mon Nov 28 2022 - 13:30:03 PST
