[gmx-users] Regarding topology creation

[Mark Abraham]

Hi,

pdb2gmx needs to know whether you intend a residue with a different number
to be a new molecule, or not. There's a standard TER field in PDB that can
be used to do that (and pdb2gmx has some command-line options that tune
that and related behaviour).

It's a bit more efficient to make an .itp for a single glycine, and craft
your .top with it by hand, than to make pdb2gmx recognize and construct an
identical topology for each glycine molecule.

Mark

On Sun, Apr 2, 2017 at 7:44 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Thank you Peter for replying..
>
> But i didnt get u ...whn i gave the gmx pdb2gmx command for one glycine
> molecule with the same above residue, it was able to create a topology file
> in Charmm FF, but with more no. of glycine molecules it is showing error..
> can u kindly explain bit ...is there any link that i should give between
> one glycine with another glycine molecule..in pdb.?? or
>
> n molecules of glycine.pdb...my 2nd glycine molecule starts with Atom
> 11 and continues...
>
> ATOM      1  N   GLY
>
> ATOM      2  H1  GLY
>
> ATOM      3  H2  GLY
>
> ATOM      4  H3  GLY
>
> ATOM      5  CA  GLY
>
> ATOM      6  HA1 GLY
>
> ATOM      7  HA2 GLY
>
> ATOM 8 C GLY
>
> ATOM      9  OT1 GLY
>
> ATOM     10  OT2 GLY
>
> ATOM     11  N   GLY
>
> ATOM     12  H1  GLY.....
>
>
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> On Sun, Apr 2, 2017 at 9:21 PM, Peter Stern <peter.stern at weizmann.ac.il>
> wrote:
>
> > Hi,
> >
> > OT1 and OT2 are only for the C-terminal amino acids and for one glycine
> it
> > is both N-terminal and C-terminal.
> > For everything else you need to use change it to O.
> > You will have the same problem with H1, etc.  Except for N-terminal aa it
> > needs to be HN.
> >
> > Regards,
> > Peter
> >
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Dilip H
> N
> > Sent: Sunday, April 02, 2017 6:23 PM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Regarding topology creation
> >
> > Hello,
> > I want to create a topology for n glycine molecules....
> > I have 1 glycine molecule and in charmm FF i am able to get the topology
> > of 1glycine molecule, but now i have few more glycine molesules in .pdb
> > format, but if i give the command gmx pdb2gmx -f gly.pdb -o gly.gro it
> > shows the following error..
> > Fatal error:
> > Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
> > while sorting atoms.
> >
> > But when i gave the same command for 1 glycine molecule to create the
> > topology, the topology file was created, but now it is not creating (for
> > more glycine molecules).. why is this happening.?? since the same OT1 is
> > also present in 1 glycine molecule, why is the above error message coming
> > for more molecules..??
> >
> > here is the 1 molecule glycine.pdb (only residue)
> >
> > ATOM      1  N   GLY
> >
> > ATOM      2  H1  GLY
> >
> > ATOM      3  H2  GLY
> >
> > ATOM      4  H3  GLY
> >
> > ATOM      5  CA  GLY
> >
> > ATOM      6  HA1 GLY
> >
> > ATOM      7  HA2 GLY
> >
> > ATOM 8 C GLY
> >
> > ATOM      9  OT1 GLY
> >
> > ATOM     10  OT2 GLY
> >
> > Thank you
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack <
> > https://mailtrack.io/install?source=signature&lang=en&
> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>