There are two problems with your input files:
In csx.ac, you have a DU atom type. There is no definition for S with three
single-bonded atoms.
In csx.mc file, you added an atom does not exist at all (OMIT_NAME H1).
After those two problems being fixed, prepgen and parmchk2 should work fine.
All the best
Junmei
On Thu, Dec 7, 2017 at 8:25 AM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> I attached my input files below. Here I am working on modified cysteine
> residue.
>
> On Thu, Dec 7, 2017 at 5:59 PM, junmwang.gmail.com <junmwang.gmail.com>
> wrote:
>
> >
> > Could you send me the input? In most cases, the incorrect/incomplete
> > input
> > causes errors.
> > Best
> > Junmei
> > Sent from my Huawei Mobile
> >
> > -------- Original Message --------
> > Subject: [AMBER] Modified amino acid
> > From: Rajarshi Roy
> > To: AMBER Mailing List
> > CC:
> >
> > I am simulating a protein structure which having a modified amino
> acid
> > residue. So I am trying to derive library file for it, but I am
> > getting
> > this following error.
> > ----------------------------------------
> > parmchk2 -i csx.prepin -f prepi -o frcmod.csx -a Y -p
> > $AMBERHOME/dat/leap/parm/parm10.dat
> > /apps/amber16/bin/parmchk2: line 4: 5567 Segmentation fault (core
> > dumped) $AMBERHOME/bin/to_be_dispatched/parmchk2 "$."
> > Can anyone help me out from this problem?
> > Thank you in advance!
> > --
> > with regards
> > Rajarshi Roy
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
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> > AMBER.ambermd.org
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> >
>
>
>
> --
>
> with regards
> Rajarshi Roy
>
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
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> AMBER mailing list
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>
>
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Received on Thu Dec 07 2017 - 08:00:02 PST
