Dear all,
I have also tried generating parameter file for the charmmlipid2amber
output provided in the test folder of AmberTools16.
The same error appears "FATAL: Atom .R<Cl- 565>.A<Cl- 1> does not have a
type."
For water, O, H1 and H2 are the atom types in residue templates and still
it does not save the prmtop file.
Any guidance is appreciated...
-Chetna
On Wed, Mar 28, 2018 at 11:41 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> Dear AMBER users,
>
> I am having exactly the same issues as Chetna with simulating a peptide
> and lipid membrane. Any insights and suggestions would be greatly
> appreciated.
>
> John
>
>
>
> -----Original Message-----
> From: Chetna Tyagi [mailto:cheta231.gmail.com]
> Sent: Wednesday, March 28, 2018 4:30 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] peptide and bilayer membrane simulations
>
> Dear all,
>
> 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.
>
> 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?
>
> Please help.
>
>
>
> --
> Best wishes
> Chetna
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--
Best wishes
Chetna
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Received on Wed Mar 28 2018 - 03:00:03 PDT
