Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber

From: Shankha Banerjee <shankhabanerjee2012.gmail.com>
Date: Sat, 7 Sep 2019 11:30:26 +0530

Thanks for your response. Please refer to the trailing mail.

My parent AA residue for this modified unit is ASP and it has been
modified by fictionalization at it's N-terminal 'N' atom. So I added
an extra oxygen atom (name O and atom number 56 in PDB file) to the C
terminal 'C' atom of the modified AA residue to complete it's
structure. I mentioned total charge as -2 (one unit of negative charge
for side chain carboxylate and one unit for C-terminal carboxylate)
and generated .ac file using antechamber, following tutorial B5. As,
the modified AA residue is at C terminal end, while I wrote .mc file,
I mentioned only TAIL_NAME, MAIN_CHAIN, OMIT_NAME, POST_TAIL_NAME and
CHARGE. Here in .mc file, I gave CHARGE -1, as there will be only side
chain carboxylate group, once this modified AA residue is connected to
a polypeptide chain.

Please find the PDB file, .ac file and .mc file, what I have used for
this modified AA residue, in attachment. Here is the error came when I
called prepgen as given in tutorial B5.

COMMAND USED- prepgen -i
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.ac -o
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.prepin -m
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.mc

ERROR MESSAGE-
POST_TAIL_TYPE is N
Net charge of truncated molecule is -1.00
TAIL_ATOM 53 C14
MAIN_CHAIN 1 45 CA
MAIN_CHAIN 2 43 N
MAIN_CHAIN 3 1 C
MAIN_CHAIN 4 3 C1
MAIN_CHAIN 5 4 C2
MAIN_CHAIN 6 7 C3
MAIN_CHAIN 7 10 C4
MAIN_CHAIN 8 15 C5
MAIN_CHAIN 9 16 C6
MAIN_CHAIN 10 19 C7
MAIN_CHAIN 11 24 C8
MAIN_CHAIN 12 25 C9
MAIN_CHAIN 13 28 C10
MAIN_CHAIN 14 31 C11
MAIN_CHAIN 15 36 C12
MAIN_CHAIN 16 37 C13
MAIN_CHAIN 17 53 C14
OMIT_ATOM 1 55 O2
Number of mainchain atoms (including head and tail atom): 17
/home/dynamix/sware/amber16/amber16/bin/prepgen: line 4: 26739
Segmentation fault (core dumped)
$AMBERHOME/bin/to_be_dispatched/prepgen "$."

Thanks,
Shankha Banerjee

> Message: 5
> Date: Fri, 6 Sep 2019 12:19:47 +0000
> From: David Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] How to generate parameter files of modified
> terminal amino acid residue using Antechamber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20190906121946.xmpoa77ja6q2pdjx.David-Case-MBP.fios-router.home>
> Content-Type: text/plain; charset="us-ascii"
>
> On Thu, Sep 05, 2019, Shankha Banerjee wrote:
>
>>But the in output PDB file, side-chain carboxylate group of ASP made a
>>five-membered ring with C-terminal carbon of ASP residue when I gave
>>net charge zero in Antechamber.
>
> You always need to give the correct net charge. If gas phase
> minimization gives geometries that one would not expect in solution, you
> can turn off minimization, and have antechamber use the input structure
> only. See Note #7 in Section 15.2 of the Amber 2019 Reference Manual.
>
> While I gave net charge as -1 and
>>multiplicity 3, the program did not run giving "fatal error".
>
> It's always helpful to give as much of the actual error message as you
> can. But antechamber charge generation is designed for closed-shell
> molecules, so setting multiplicity to 3 won't do what you want.
>
> ...hope this helps...dac
>
>
>
>
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> End of AMBER Digest, Vol 2758, Issue 1
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Received on Fri Sep 06 2019 - 23:30:02 PDT
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