Re: [AMBER] Library for Phosphate ion

From: Sowmya Indrakumar <>
Date: Wed, 1 May 2019 13:19:14 +0000

Dear Prof. Case,

Thanks a lot for your comments.

Using gaff2 and running minimization without any restraints works fine.



From: David A Case <>
Sent: Wednesday, May 1, 2019 1:44:06 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Library for Phosphate ion

On Wed, May 01, 2019, Sowmya Indrakumar wrote:
>I'm trying to simulate my protein in 140mM Phosphate molecules. I'm
>able to generate the *.lib and *.frcmod files using antechamber by
>taking some information from $AMBERHOME/dat/leap/lib/phos_amino94.lib
>and frcmod.phosaa10 files. I have attached the generated force-field,
>molecule.mol2 and library file to this email.
>At the minimisation step, it crashes after 1000 steps with these energy values in the last step.
>VDWAALS = 51536.5780 EEL = -660193.0656 HBOND = 0.0000
> 1-4 VDW = 2450.2952 1-4 EEL = -6065531.1803 RESTRAINT = 0.0000
> 1000 -2.9076E+07 1.7146E+10 5.8700E+12 H7 10804
> BOND = 30727.5122 ANGLE = 4063.7483 DIHED = 7122.5793
> VDWAALS = 51536.5780 EEL = -660193.0656 HBOND = 0.0000
> 1-4 VDW = 2450.2952 1-4 EEL = ************* RESTRAINT = 0.0000

Check your final structure. As a guess, the most likely problem is that
one of the protons on a phosphate has become very close to a neighboring
oxygen on the same phosphate. Also check atom 10804, to see what its
environment is.

The frcmod file you use has special angle terms to try to eliminate this
problem, but you may need to use GAFF2 which assigns non-zero
Lennard-Jones parameters to protons on phosphates. A lot depends on
what is causing the problem.

Be sure you are using SHAKE during your minimization. You might also
try a low-temperature MD in the place of minimization: that is sometimes
more stable.

An alternative is to add a pseudo bond between P and H, to keep the
phosphate ion more rigid.

...good luck....dac

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