Hi Ben?
I found the most answers to my previous questions at http://salilab.org/modeller/FAQ.html#8
The Charmm parameter and topology for ligand were successfully generated with all Hydrogens by swissparam server.
I follow the instructions and edit the files: top_heav.lib, radii.lib, radii14.lib, solv.lib and restyp.lib, where my ligands were defined has one letter code "8".
See the end of the alignment (*.pap):
_aln.pos 270 280 290
1HVY KIDDFKAEDFQIEGYNPHPTIKMEMAV8
TS-Tgondii EIDDFTAEDFEVVGYVPHGRIQMEMAV8
_consrvd **** **** ** ** * ******
After build models with "allhmodel" options, i saw that the ligand in models remains unchanged. Its like It was defined it as BLK "."
Ligand position and interactions were not optimized.
All amino acids residues have hydrogens but the ligand not, in spite of all ligand hydrogens are present in its topology at top_heav.lib.
Which file must I edit to set the parameter for lgiand? par.lig, par_all22_prot_b5.inp or par19.inp?
What is missing?
Regards,
Flavio
--- On Thu, 12/6/12, flavio seixas <> wrote:
> From: flavio seixas <>
> Subject: [modeller_usage] Protein-ligand simulate annealing
> To: "Modeller Usage" <>
> Date: Thursday, December 6, 2012, 7:17 PM
> Hi Ben
>
> I successfully generate charmm force fields (parameter and
> topology files) using swissparam server, for the ligand that
> is bonded to my protein template.
>
> Now I want to built models bonded to this ligand and also
> optimize them using Modeller protocol for MD and SA.
>
> My questions are:
>
> 1) How can I make modeller reads the parameter and topology
> files for the ligand? Is there a command for it?
>
> 2) Or should I copy and paste the ligand topology data to
> top_heav.lib file?
>
> 3) If the second option is the choice, where to paste the
> information regarding the parameters?
>
> 4) In the alignment file, how to set the symbol for the
> ligand? I think if I set it as BLK "." no changes will be
> made. Is that right?
>
> Best regards,
>
> Flavio
>
>
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