[gmx-users] Regarding topology creation

[Dilip H N]

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