Dear David,
Thank you for this help. And that's a great news about membrane builder
program additions.
-Chetna
On Wed, Mar 28, 2018 at 3:56 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Mar 28, 2018, Chetna Tyagi wrote:
> >
> > As I wrote earlier, I want to simulate a peptide and lipid membrane. The
> > peptide does not need to be inserted. This peptide has engineered
> residues.
> >
> > The charmmlipid2amber.py script does not work even when I chose
> > membrane-only system generated by CHARMM-GUI. The prmtop file is not
> saved
> > with errors like below.
> >
> >
> > FATAL: Atom .R<WAT 385>.A<O 1> does not have a type.
> > Failed to generate parameters.
> >
> > I see that these errors erupt over only water and K+, Cl- atoms. I always
> > upload the "loadamberparams frcmod.ionsjc_tip3p" and even tried with
> > solvents.lib.
>
> What you should be loading is leaprc.water.tip3p: that has everything
> one needs for tip3p water + ions (with parameters compatible with
> tip3p).
>
> >
> > Is there a way to build lipids around or nearby the peptide using only
> > AmberTools? So that I do not have to struggle with conversion?
>
> I know this doesn't help much now, but in the upcoming AmberTools18
> release (due out in a few weeks) there will be two(!) membrane/bilayer
> building programs.
>
> ....dac
>
>
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>
--
Best wishes
Chetna
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Received on Wed Mar 28 2018 - 09:00:02 PDT
