On Sat, Mar 03, 2018, Rana Rehan Khalid wrote:
> After pdb file editing according to .prep file of GTP following messages
> shown
>
> Loading PDB file: ./dimer-GTP.pdb
> One sided connection. Residue: default_name missing connect1 atom.
> One sided connection. Residue: TP3 missing connect0 atom.
> total atoms in file: 6169
> Leap added 7 missing atoms according to residue templates:
> 7 H / lone pairs
>
> log file shows
>
> Starting new chain with MG
> One sided connection. Residue: default_name missing connect1 atom.
> One sided connection. Residue: TP3 missing connect0 atom.
> Starting new chain with TP3
> Starting new chain with TP3
> total atoms in file: 6169
> Leap added 7 missing atoms according to residue templates:
> 7 H / lone pairs
>
> kindly guide how to resolve this connection issue. Thanks
These look like informational messages, not errors. Did you get a prmtop
file? You can use parmed to examine it, to see if it has the bonding you
expect?
[The message about "residue: default_name missing connect1 atom" is, however,
of concern: do you have anything that that might be called "default_name"?
How did you load parameters for MG?]
....dac
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Received on Sat Mar 03 2018 - 14:30:03 PST
