Sure.
I did "cpptraj -p ../complex_solv1.prmtop"
When cpptraj starts up, I get the following errors:
Error: Atom 8770 was assigned a lower molecule # than previous atom. This
can happen if 1) bond information is incorrect or missing, or 2) if the
atom numbering in molecules is not sequential. if topology did not
originally contain bond info, 1) can potentially be fixed by increasing the
bondsearch cutoff offset (currently 0.200). 2) can be fixed by either using
the 'fixatomorder' command, or using the 'setMolecules' command in
parmed.py.
Error: Could not determine molecule information for ../complex_solv1.prmtop
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for ../complex_solv1.prmtop
Then I did:
trajin heat_all.mdcrd
trajin eq.mdcrd
trajout eq-wrapped.mdcrd
center :1-574
image familiar
go
Then I get the following output:
ACTION SETUP FOR PARM '../complex_solv1.prmtop' (2 actions):
0: [center :1-574]
Mask [:1-574] corresponds to 8769 atoms
1: [ image familiar]
Warning: Mask '*' selects no atoms for topology '../complex_solv1.prmtop'.
Warning: Setup failed for [image familiar]: Skipping
Residues 1-574 correspond to the protein atoms. Residue 575 is the heme,
and atom 8770 is the heme iron atom.
Thanks,
Arjun
On Mon, Mar 7, 2016 at 10:44 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Mar 4, 2016 at 9:26 AM, Arjun Narayanan <arjun.nufc.gmail.com>
> wrote:
> > I ran the simulation and got errors in cpptraj
> > trying to image atoms back into the box. This (as I found out in
>
> Can you be more specific about what errors you received from cpptraj?
> Maybe I can help address the original problem.
>
> -Dan
>
> > retrospect) has been well-documented on this mailing list previously.
> >
> > >From my understanding, the solution was to re-setup my system using the
> > setMolecules command in parmed.py. I did this, but when I loaded the new
> > prmtop and restrt file into VMD there were a lot of badly distorted bonds
> > with extremely long bond lengths. I confirmed this by loading these back
> > into parmed.py and using the checkValidity command. In particular, I get
> > errors such as the following:
> >
> > LongBondWarning: Atoms (X) and (Y) are bonded ... but are 43.057 A
> apart.
> > This often indicates gaps in the original sequence and should be checked
> > carefully.
> >
> > Has anyone observed this before? And what actions can I take to resolve
> > this?
> >
> > Thanks for any help in advance,
> >
> > Arjun Narayanan
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 07 2016 - 08:30:03 PST
