Hi Case,
Thank you so much for your generous reply. I tried your methods,
however, depressingly, they could not work. I used the "-nc 1" to
tell antechamber this ligand has net charge 1. But antechamber failed
when going to sqm. Here is the error message:
Running: /home/crystal/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: Bond types are assigned for valence state 1 with penalty of 1
Running: /home/crystal/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 178; net charge: 1
Running: /home/crystal/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/crystal/amber11/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit
I checked the structure of the ligand, and realized the two oxygen of
phosphate group had no hydrogen. Besides, one oxygen should be double
bond. I do not know if no hydrogen on oxygen of phosphate caused the
problem of running antechamber, so I trid Chimera to add H. But
Chimera does not add H to these two oxygen. Do you know how I can add
H to these two oxygen atom?
I also followed the method provide by the link. Since my ff99SB uses
ions94.lib, so I change ions94.cmd. But after changing ions94.cmd and
typing "tleap -f ions94.cmd", xleap still fails to generate prmtop and
inpcrd. Here is the original script of ions94.cmd:
i = createAtom MG MG 2.0
set i element Mg
set i position { 0 0 0 }
r = createResidue MG2
add r i
MG2 = createUnit MG2
add MG2 r
saveOff MG2 ./ions94.lib
And this is the modified version, changing MG to Mg+:
i = createAtom Mg+ MG 2.0
set i element Mg
set i position { 0 0 0 }
r = createResidue MG2
add r i
MG2 = createUnit MG2
add MG2 r
saveOff MG2 ./ions94.lib
Do you know if there are other possible methods to solve this problem?
Thank you for your suggestions again.
Sincerely,
Crystal
On 11/11/11, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Nov 11, 2011, Crystal.CHIA-YU Ku wrote:
>>
>> xleap seems like not to recognize Mg2+ ions, and my ligand TPS.
>>
>> Total number of electrons: 179; net charge: 0
>> Please check the total charge (-nc flag) and spin multiplicity (-m
>> flag)
>
> Antechamber only works for closed shell molecules. Two things to check:
>
> 1. Does your ligand have a net charge? If so, you need to use the "-nc"
> flag
> to antechamber to tell the program the total charge of the ligand, since the
> default value is zero.
>
> 2. If that doesn't help, double check the input structure carefully. Make
> sure all hydrogen atoms are present, and that the structure is consistent
> with
> a closed shell neutral molecule.
>
> Amber doesn't really have any default Mg2+ ion parameters. For a
> workaround,
> check this link: http://archive.ambermd.org/201111/0020.html
>
> ....good luck....dac
>
>
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Received on Fri Nov 11 2011 - 18:00:03 PST
