[gmx-users] Cytochrom C

[Dariush Mohammadyani]

Dear Justin,

You are right, I had some warning and with -missing I override them, e.g.:

WARNING: atom HA is missing in residue HEM 105 in the pdb file
WARNING: atom HB is missing in residue HEM 105 in the pdb file
...

30 missing atoms. I did not know how should figure them out. I am using
GROMACS 4.5.3
and charmm27.ff.
Cytochrome C is a difficult protein to simulate :(

Thanks,
Dariush





On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Dariush Mohammadyani wrote:
>
>> According your help and "pdb2gmx -his -missing" I could create input
>> files. Also I used grompp without error. However, for mdrun I got this
>> error:
>>
>
> Using the -missing flag is very dangerous.  If you're using it to override
> warnings or errors that pdb2gmx is giving, your simulations will almost
> certainly be junk because the topology is broken.
>
>  *Function type CMAP Dih. not implemented in ip_pert*
>>
>>
>> How can I figure it out?
>>
>>
> Without seeing your .mdp file and knowing which Gromacs version you're
> using, there's little anyone can do to help you.  The error suggests you're
> trying to transform a CMAP dihedral using the free energy code, which
> cannot be done (per the error message).
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120117/3a3b60d6/attachment.html>