Thanks! That actually gives me the following error:
| INFO: Old style PARM file read
forrtl: severe (64): input conversion error, unit 10, file /afs/
crc.nd.edu/user/s/ssensale/Documents/Try2/sequence.pdb
Image PC Routine Line Source
libifcore.so.5 00007F98AAE73C60 Unknown Unknown Unknown
libifcore.so.5 00007F98AAE71444 Unknown Unknown Unknown
ambpdb 000000000040650D Unknown Unknown Unknown
ambpdb 0000000000401F22 Unknown Unknown Unknown
ambpdb 00000000004011E6 Unknown Unknown Unknown
libc.so.6 0000003E6421ED1D Unknown Unknown Unknown
ambpdb 00000000004010D9 Unknown Unknown Unknown
On Mon, Nov 21, 2016 at 2:29 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> you can use a pdb file that match the atoms in your prm file and use that
> pdb for topology
>
> ambpdb -p your.pdb < your.rst > your_new.pdb
>
> Hai
>
> On Mon, Nov 21, 2016 at 2:21 PM, The Cromicus Productions <
> thecromicusproductions.gmail.com> wrote:
>
> > Hi everyone,
> >
> > Is there any way of converting prm files into prmtop?
> > A colleague of mine works in NAMD and he gave me a bunch
> > of simulations of which I want to get the pdb file associated to the
> > final screenshot. I have the dcd files (Which I convert to mdcrd and
> > then I save the final screenshot as a .rst file) and then the prm files
> > (which I guess I should convert to prmtop).
> > My idea was to use a command as in the tutorial:
> > $AMBERHOME/bin/ambpdb -p polyAT_vac.prmtop < polyAT_gb_init_min.rst >
> > polyAT_gb_init_min.pdb
> >
> > but I have a bunch of prm files
> > par_all36_carb.prm
> > par_all36_cgenff.prm
> > par_all36_lipid.prm
> > par_all36_na.prm
> > par_all36_prot.prm
> >
> > Is there any way to work with this?
> > Thanks a lot!
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 21 2016 - 12:00:02 PST
