AMBER Archive (2009)

Subject: Re: [AMBER] broken Ligand

• Previous message: xueqin pang: "[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy"
• In reply to: Shubhra Gupta: "Re: [AMBER] broken Ligand"
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On Sat, May 30, 2009, Shubhra Gupta wrote:
>
> Sorry for sparse information. I have attached the files. a.pdb file I got
> after saving topology (a.prmtop) and parameters (a.inpcrd). I Sourced
> leaprc.GLYCAM_06 and leaprc.gaff. For solvation I used TIP3PBOX and 7.0
> buffer. min.in was input file to execute sander for minimization. Resulted
> a_min.pdb is after minimization, where the ligand is broken.

I don't see what is "broken" in the a_min.pdb file, but that is OK:
since you know what the problem seems to be, you can debug for yourself.
Your files show a periodic system with explicit water, but the min.in file is
for a non-periodic system using GB. Try doing just a gas-phase minimization
on the 4YA residue all by itself. If you have problems, make is smaller until
things work, and then try to build back up to the full ligand molecule.

...dac

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• Previous message: xueqin pang: "[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy"
• In reply to: Shubhra Gupta: "Re: [AMBER] broken Ligand"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]