Yes sir I got the prmtop and card files, as in different thread you guide ,
I source the leaprc.water.tip3p it have Mg, so I do not add any other
parameter file for Mg. Could you please guide me what do you mean about
"""[The message about "residue: default_name missing connect1 atom" is,
however, of concern: do you have anything that that might be called
"default_name"? ""
I do not get that point
Kind Regards
Khalid
On Mar 4, 2018 12:26 AM, "David A Case" <david.case.rutgers.edu> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 03 2018 - 15:00:02 PST
