Dear Irene Newhouse
That's an easy problem.
*I'm sorry, in my case I use xleap.
When you use xleap (tleap), you check the list (comand :list on the
xleap)
We can use only molecules in the list.
So you check the pdb format on your pdb data
COLUMNS DATA TYPE FIELD DEFINITION
------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in
Angstroms
39 - 46 Real(8.3) y Orthogonal coordinates for Y in
Angstroms
47 - 54 Real(8.3) z Orthogonal coordinates for Z in
Angstroms
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
77 - 78 LString(2) element Element symbol, right-
justified.
79 - 80 LString(2) charge Charge on the atom.
Example
1 2 3 4 5 6
7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00
11.92 N
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00
11.85 C
ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00
12.34 C
ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00
15.65 O
I think leap program reads a Residue name (ex:VAL).
Therefore
in your case
> HETATM 3092 MG2 IP D 206 32.173 43.347 19.203 0.50
> 27.35 Mg2+
you change
HETATM 3092 MG MG2 D 206 32.173 43.347 19.203 0.50 27.35
$B"*(Byou change IP to MG2
...good luck...
Takeshi Baba
On 2011/07/01, at 6:24, Irene Newhouse wrote:
>
> I'm trying to do MD of a protein complexed with Mg-ATP, and I'm
> having difficulty processing the MG through tleap. I'm using prepi/
> frcmod files for ATP from the work of Carlson & al, which was
> recently discussed on this mailer [thanks so much!] From grepping
> around the /dat/leap dirs of amber11, I've deduced that the atom
> name for MG should be MG2. But I have no idea what to call the
> residue name. I've tried:
>
> HETATM 3092 MG2 IP D 206 32.173 43.347 19.203 0.50
> 27.35 Mg2+
>
> and I've tried leaving the residue name field blank. Both instances
> result in the same leap message [with IP replace by spaces in the
> other case]:
>
> Creating new UNIT for residue: IP sequence: 206
> Created a new atom named: MG2 within residue: .R<IP 206>
>
> When I try to write prmtop/inpcrd files at the end of my processing,
> I get:
> FATAL: Atom .R<IP 206>.A<MG2 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Yes, I did load the forcefield [I work from pre-written scripts as
> much as I possibly can, since I'm prone to stupid typing errors].
> What do I do now? Thanks!
>
> Irene Newhouse
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
----------------------------------------------------------------------------------------------------
Takeshi Baba
Graduate School of Life Science, University of Hyogo,
3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
E-mail: tbaba.cheng.es.osaka-u.ac.jp
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Received on Thu Jun 30 2011 - 18:30:03 PDT
