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
On Sat, Mar 3, 2018 at 5:27 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> This can't be ignored. You loaded GTP parameters, but you have something
> called GSP in your coordinates file that does not match any residue name in
> the force field. You need to find out what GSP is and either name it
> properly to match the residue name in the parameter file, or load GSP
> parameters.
>
> On Mar 3, 2018 5:43 AM, "Rana Rehan Khalid" <rrkhalid.umich.edu> wrote:
>
> Dear amber users
> I loaded the GTP.prep and frcmod.phos in tleap, but when I load pdb file
> these error messages showed. Kindly guide How i can resolve it. Thanks
>
>
> Unknown residue: GSP number: 395 type: Nonterminal
> Creating new UNIT for residue: GSP sequence: 396
>
> Created a new atom named: N9 within residue: .R<GSP 396>
> Created a new atom named: C8 within residue: .R<GSP 396>
> Created a new atom named: N7 within residue: .R<GSP 396>
> Created a new atom named: C5 within residue: .R<GSP 396>
> Created a new atom named: C6 within residue: .R<GSP 396>
> Created a new atom named: O6 within residue: .R<GSP 396>
> Created a new atom named: N1 within residue: .R<GSP 396>
> ;
> ;
> total atoms in file: 6170
> Leap added 6 missing atoms according to residue templates:
> 6 H / lone pairs
> The file contained 44 atoms not in residue templates
>
> regards
> khalid
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Received on Sat Mar 03 2018 - 10:00:02 PST
