Hi Case,
In ions94.cmd, I modified first MG to Mg+ in "createAtom" after
comparing with ions the link you provided:
http://archive.ambermd.org/201111/0020.html. The second MG in
ions94.cmd has the same format as that you suggested in the link, so I
just modified the first MG which is the only difference between
ions94.cmd and ions08.cmd. The I typed the command: tleap -f
ions94.cmd. But this modification and commond could not let xleap
recognize my Mg ions and failed to generate prmtop and inpcrd files. I
provided the modified part of my ions94.cmd.
I tried desc to find how xleap recognized MG.1 in my receptor. The
result is disappointing. First, xleap cannot give 2+ charge to MG.
Second, xleap seems to detect the first Mg ion at residue 89 (xleap
names the two stand-alone Mg ions as residue 89 and 90.). I pasted the
command and output after the information of ions94.cmd, and attach the
leap.log as your reference.
Besides, I describe the way after the informatio of desc to obtain
the receptor-ligand files. The manipulation includes: adding H by
Chimera, deleting Mg connectvity to residues and ligands, and taking
off unnecessary Mg2+, Ca2+ ions, and water. I attached the
receptor-ligand file as your reference.
Thank you and other amber users so much for your generous suggestions
in advance.
Sincerely,
Crystal
========Information about ions94.cmd====================
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 the first 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
=======================================================
=========Information about desc command=====================
> 2hom=loadpdb "2HOM_1_addH.pdb"
> saveamberparm 2hom test.prmtop test.inpcrd (fail.....)
> desc 2hom.MG.1
ATOM
Name: MG
Type:
Charge: 0.0000
Polarization: 0.0000
Element: Mg
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 31.301000, 36.964000, 68.260000
Atom velocity: 0.000000, 0.000000, 0.000000
NO BONDS
> desc 2hom.MG
RESIDUE name: MG
RESIDUE sequence number: 89
RESIDUE PDB sequence number: 81
Type: undefined
Connection atoms:
Improper torsions:
Contents:
A<MG 1>
=======================================================
=========method to obtain my receptor-ligand file=================
1. Copy the crystal structure information fo the orignal file to an
empty file, and name as 2HOM_MD.pdb
2. Open 2HOM_MD.pdb by Chimera, then add H to the receptor and ligand.
Save it as 2HOM_1_addH.pdb
3. Open 2HOM_1_addH.pdb by gedit. Directly delete all water moleculesm
Mg2+, Ca2+ ions, except HETATM 2540 MG and HETATM 2541 MG. Then delete
the connectivity of ligand and residues of receptor to HETATM 2540 MG
and HETATM 2541 MG.
4. Save the manipulation in 2HOM_1_addH.pdb
=============================================================
On 11/15/11, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Nov 14, 2011, Crystal.CHIA-YU Ku wrote:
>>
>> MG ion is another problem when I load pdb file of my receptor-ligand
>> pair, xleap cannot recognize two MG ions and the ligand. I tried to
>> remove the connectivity of the two MG ions, which means I let two MG
>> ions stand alone. But this way has not worked. I also modifed the
>> ions94.cmd; however, this way has not made success. I always get error
>> message like this:
>> FATAL: Atom .R<MG 89>.A<MG 1> does not have a type.
>> FATAL: Atom .R<MG 90>.A<MG 1> does not have a type.
>
> We need more details, about exactly what commands you gave, how you modified
> ions94.cmd, etc. It often helps to use the "desc" command in LEaP to see
> what is inside your units, e.g. "desc MG.1" will give you a list of the atom
> names and types.
>
> ...dac
>
>
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Received on Tue Nov 15 2011 - 16:00:08 PST
