Re: [AMBER] Problem with bonds in NAB

From: David A Case <>
Date: Thu, 24 Nov 2016 13:58:09 -0500

On Thu, Nov 24, 2016, Vladislav Sláma wrote:

> I have tried whole process of parametrization and minimization with standard
> GAFF atom types. First I have generated mol2 file from output of Gaussian
> esp calculation with:
> antechamber -i FGrph-5hex_esp-charges-ini.esp -fi gesp -o FGrph-5hex.mol2
> -fo mol2 -c resp -eq 0 -at gaff -rn FGR
> Than I have checked if all parameters for my system are defined in GAFF with:
> parmchk -i FGrph-5hex.mol2 -f mol2 -o FGrph-5hex.frcmod
> and there was no need to add any new parameters. Then I have created
> parameter and coordinate file with tleap:
> source leaprc.gaff
> FGR=loadmol2 FGrph-5hex.mol2
> loadamberparams FGrph-5hex.frcmod
> saveamberparm FGR FGrph-5hex.prmtop FGrph-5hex.inpcrd
> savepdb FGR FGrph-5hex.pdb

Can you post the FGrph-5hex.prmtop and FGrph-5hex.inpcrd files? Those are the
ones we need to reproduce the problem.

As before, it is of little use in debugging to compare the minimized
structures. You (or we) need to see the energies at the initial step, and
figure out why they are different.

Posting the frcmod file might also be helpful.


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Received on Thu Nov 24 2016 - 11:00:04 PST
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