AMBER Archive (2009)

Subject: AW: [AMBER] atomtypes in gaff

From: Aust, Susanne (
Date: Thu Jun 25 2009 - 07:05:10 CDT

You are too fast,

I don't use a script.
i will write down, what I do.
1) source leaprc.ff03
2) source leaprc.gaff
3) loadoff ZNA.lib
4)loadamberparams zna.frcmod
5)loadamberparams bzim_correct.frcmod
6) loadamberprep bzim_correct.prepin
7)test=loadpdb "c2k_bzim_correct.pdb"
8)addions test Cl- 0
9) solvateoct test TIP3BOX 8.0
10) saveamberparm test test.prmtop test.inpcrd

and here are the files.

-----Ursprüngliche Nachricht-----
Von: []Im
Auftrag von FyD
Gesendet: 25 June 2009 13:45
An: AMBER Mailing List
Betreff: Re: [AMBER] atomtypes in gaff

Quoting "Aust, Susanne" <>:

Could you send me your LEaP script (that used to generate your
prmtop/prmcrd files) + Zinc library (mol2 file format) + FF library
for your benzimidazole-structure (mol2 file format) + the structure of
your complex (PDB file format).

regards, Francois

> I load the complex in xleap as pdb, so no name is necessary.
> At my first trail I load the wrong pdb with ZNB in the pdb. I correct this
> ZNA (like in my ZNA.lib) and load the pdb again and then everything was
> in without error.
> The ligand in the complex has the name ABI. The parameter for this ligand I
> read in to xleap with loadamberparams bzim_correct.frcmod and loadamberprep
> bzim_correct.prepin.
> When I prepare my complex in xleap, there is no error and the pdb or mol2
> from xleap looks o.k.
> But after the minimization the ligand is not coordinated. With a wrong
> benzimidazole-structure (the double bonds are not on the correct positions)
> the ligand keeps coordinated.
> It's difficult for me, to describe the problem, because I don't know
> at which position of the preparation line the failure occurs.
> regards,
> Susanne
> -----Ursprüngliche Nachricht-----
> Von: []Im
> Auftrag von FyD
> Gesendet: 25 June 2009 12:33
> An: AMBER Mailing List
> Betreff: Re: AW: [AMBER] atomtypes in gaff
> Susanne,
> You need to add a molecule name to your Tripos mol2 file (I wonder if
> this is not a bug in the savemol2 command because you have many
> residues...):
> C2K
> 3263 3293 228 0 1
> etc...
>> The atomtypes should be correct.
>> I send you the mol2 file of the comlex from xleap.
>> The benzimidazole is over the N3 (nd) non physical coordinated to the
>> I calculate other ligands (substrate and imidazole derivative) with this
>> enzyme and it works.
>> So I think it is not a problem of zinc.
>> I hope, this is the file you want.
>> I send you also the xleap.log
> In your LEaP log file, you load the Zinc FF library:
> loadoff ZNA.lib
> In your Tripos mol2 file, your Zinc is defined as ZNB (residue name,
> FF atom type & atom name). Consequently, in LeaP you get this message:
> Unknown residue: ZNB number: 225 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> (Residue 226: ZNB, Terminal/last, was not found in name map.)
> Unknown residue: ZNB number: 226 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Then, you load the frcmod file for your zinc atom:
> Loading parameters: ./frcmod.zna
> Reading force field modification type file (frcmod)
> Reading title:
> This frcmod file is for ZNA (zinc 2+ ion).
> I wonder if the FF atom type of Zn is well defined.
> => add
> addAtomTypes {
> { "ZN" "Zn" "sp3" }
> ^^^^
> or what is required...
> }
> I do not know if these are the reasons of your problem. However, you
> might correct these problems to see if this helps.
> regards, Francois
> _______________________________________________
> AMBER mailing list
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> AMBER mailing list

           F.-Y. Dupradeau

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