[chimera-dev] Following on new atom types.

[Eric Pettersen]

On Mar 14, 2013, at 9:23 AM, Elaine Meng wrote:

> Hi JD,
> It might work only if the Pt was treated only as a monatomic ion.  In that case you specify charge directly, but the dialog may only allow integral charges.   You can set it to any value with "setattr," however, for example if the atom was named PT: 
> setattr a charge 0.85 @PT

I think Elaine's right here.  The only way you are going to get this to work in Chimera without a Herculean amount of effort is to break the four bonds to the platinum and treat the system as a metal ion surrounded by four negative ion species and minimize that.  Then if you really need the bonds to exist for whatever reason afterward, just create them again.

Otherwise not only do you need to assign partial charges to each atom yourself, you also need to create bond, angle, and torsion parameters for Pt, since none exist in the standard Amber parameter files.  Ugh.

BTW, the "Atom whose IDATM type has no equivalent Sybyl type" message occurs whenever Chimera writes out a Mol2 file containing atoms (such as platinum) that have no equivalent Sybyl type.  In such cases the element name is written out instead.  You are probably getting this message as the Mol2 input for Antechamber is being written by Chimera.

--Eric

> 
> More about user-specified charges: 
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>
> 
> However, my understanding is that if you are defining a residue that contains the Pt (i.e. the Pt has covalent bonds to other atoms as in cisplatin), it will try to go through Antechamber.  That program is meant only to handle small organic molecules like most drugs, not metal-containing compounds or unstable species like radicals.   Further, at some step it uses SYBYL atom types, and those do not include platinum.  Although they do include some metals,
> <http://www.tripos.com/mol2/atom_types.html>
> I doubt residues with any metal would be handled well by the Antechamber calculations.
> 
> We are not the developers of MMTK (used for minimization in Chimera), Antechamber, or SYBYL, so have very limited ability to do anything about these restrictions.
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Mar 14, 2013, at 7:16 AM, Jean-Didier Maréchal wrote:
> 
>> Hi,
>> 
>> I am following on Elisabeth's question on the 23rd of january regarding setting up new atoms. I have added platinum (for cisplatinum) as a new atom type and proceed as you recommended (calculate the charge on isolated species and generate the covalent bond for the first coordination sphere of the metal). I have though two questions:
>> 
>> 1. when running the minimization I have the following message:
>> 
>> Atom whose IDATM type has no equivalent Sybyl type: #-2147483648.-2147483648:1 at PT1-CPT (type: Pt)
>> 
>> Although the minimization still proceed, I'd like to do things right. Could you tell me where I could change the sybyl atomtype. I looked with the idle the idatmType of this atom and it gives me Pt+. I don't understand what is wrong.
>> 
>> 2. I'd like to rapidly change the charges of the cisplatinum using charges calculated with ab initio calculations. I was thinking to change these values from the idle changing the charge attribute previous to minimization. Does it sound correct? What would be the easiest way you would reckon?
>> 
>> Best regards,
>> JD
>> 
>> 
>> ****************************
>> Dr. Jean-Didier Maréchal
>> Associate professor
>> The Computational Biotechnological Chemistry Team
>> Unitat de Química Física
>> Departament de Química
>> Universitat Autònoma de Barcelona
>> Edifici C.n.
>> 08193 Cerdanyola (Barcelona)
>> Tel: +34.935814936
>> e-mail: JeanDidier.Marechal at uab.es
>> www: http://gent.uab.cat/jdidier
>> _______________________________________________
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> 
> 
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