Thanks for the reply, and sorry for bothering you
I fixed my csx.mc file. How do I fix my csx.ac file?
On Thu, Dec 7, 2017 at 9:19 PM, Junmei Wang <junmwang.gmail.com> wrote:
> 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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> > >
> >
> >
> >
> > --
> >
> > with regards
> > Rajarshi Roy
> >
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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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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Received on Fri Dec 08 2017 - 02:30:02 PST
