Re: [AMBER] solid surface simulation in amber

From: David A Case <>
Date: Thu, 18 Aug 2016 09:13:05 -0400

On Thu, Aug 18, 2016, Neha Gandhi wrote:
> I have a pdb file of a unit cell and I am converting using antechamber to
> mol2 file

It sounds like the problem might be right here: how did you get this file?
Are you sure that the unit cell parameters (in the CRYST1 line) are correct?

> I prepare supercell from the input file which has unit cell information
> PropPDB -p input.pdb -o supercell.pdb -ix 15 -iy 9 -iz 4
> >>$AMBERHOME/bin/tleap -s -f leaprc.ff99SBildn
> >source leaprc.hap
> >loadamberparams frcmod.hap
> >loadoff hap.lib
> >m1=loadpdb supercell.pdb
> >set m1 box {145 150 39}

The "supercell.pdb" file should already
have the proper Unit Cell values. Are they different than {145 150 39}?
> cpptraj -p supercell.prmtop -i
> ---
> trajin correct.inpcrd
> check reportfile report.dat
> The report.dat file is empty so I assume there are no overlaps.

I agree that this is very odd, given the huge vdW energy on the first step
of minimization.

> I try to run minimization using pmemd.MPI and that's where I am not able to
> figure out why the structure shows high energies and min.rst file doesn't
> look right. I convert min.rst file using cpptraj to pdb. It seems that
> calcium ion (NG) is interpreted as carbon or some other atoms ...

Can you say what it is about the PDB file that led you the think that the
calcium ion is interpreted as carbon? PDB files have the element at the far
right of the ATOM card...what does that show?


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Received on Thu Aug 18 2016 - 06:30:03 PDT
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