Re: [AMBER] Error in conversion from charmmgui to AMBER format

From: Sally Pias <sallypias.gmail.com>
Date: Mon, 28 Jan 2019 14:35:09 -0700

Hi Souvik,

This kind of error may indicate missing TER cards between the lipid
molecules, or it may indicate that the atom order in the PDB file has been
rearranged. I have seen similar behavior many times in our own work, but it
may occur for different reasons. I think Leap is comparing the residue
topology in the PDB file to the Lipid17 residue template and finding a
difference. I may need to see your PDB file, to help further. If you wish,
you may send it to me individually, apart from the mailing list.

Best,
Sally

--
Sally Pias
Associate Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
On Thu, Jan 24, 2019 at 5:21 PM Souvik Dey <sdey8.uic.edu> wrote:
> Hi All,
>
> I am trying to convert a protein lipid system that was generated from
> CHARMM-GUI into Amber format. So, initially I used charmmlipid2amber.py
> script which runs fine.
>
> Then, I remove the hydrogen atoms from the pdb using pdb4amber. It shows no
> error.
>
> I also modify the name of Histidine and change a naming convention for ILE.
>
> However, when I try to run tleap using lipid17 and Amber14SB force field, I
> get the following error:
>
> *Error: Comparing atoms*
> *        .R<OL 3>.A<C13 11>, *
> *        .R<OL 3>.A<H2R 9>, *
> *        .R<OL 3>.A<H2S 10>, and *
> *        .R<PE 2>.A<C21 32> *
> *       to atoms*
> *        .R<OL 3>.A<C13 11>, *
> *        .R<PA 1>.A<C12 44>, *
> *        .R<OL 3>.A<H2S 10>, and *
> *        .R<PE 2>.A<C21 32> *
> *       This error may be due to faulty Connection atoms.*
> *!FATAL ERROR----------------------------------------*
> *!FATAL:    In file [chirality.c], line 142*
> *!FATAL:    Message: Atom named C12 from PA did not match !*
> *!*
> *!ABORTING.*
>
> Could someone please guide me as to where i am going wrong? Do I need to
> modify something in the charmmlipid2amber.py file?
>
> Thanks in advance.
>
> Regards,
> Souvik
> ----------------------------------------------------------
> Souvik Dey
> Graduate Student
> Department of Chemistry
> University of Illinois Chicago
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Received on Mon Jan 28 2019 - 14:00:03 PST