AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Wed Sep 16 2009 - 12:14:46 CDT

Thanks Francois
What I am trying to do is build one topology file and one inpcrd file containing both ligand (dCTP) and protein. I believe I then need to load leaprc.ff03 followed by dCTP2.mol2 whose atom names have to match those in my protein/ligand PDB file (crystal structure)...right?

The problem I ran into was that using the dCTP2.mol2 atom names which are not unique was not working. That is, just calling all phosphates "P" in my protein/ligand PDB file (making it the same names as those of the dCTP2.mol2 file) fails to work. So, I guess I need to rename atom names in dCTP2.mol2 and make them correspond to those *unique* atom names in my ligand(dCTP)/protein file..right?

Thanks, Steve

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of FyD
Sent: Wednesday, September 16, 2009 1:00 PM
To: AMBER Mailing List
Subject: RE: [AMBER] database

Steve,

As you have Cornell et al. FF atom types in this dCTP2.mol2 FF
library; loading ff03 & then using the saveamberparm command will
work. You do not need to create a new frcmod file (there is no missing
FF parameters).

You can use mol2 file format instead of prep and PDB file format.

If you want to replace Cartesian coordinates available in the mol2
file by these available in a PDB file, you need to have the same
residue names & atom names in the PDB & Tripos mol2 files.

regards, Francois

> The error I get is "20 atoms not is residue templates". However, the
> naming between the ligand.mol2 and the ligand.pdb file are the
> same. See attachments. The ligand.mol2 has hydrogens while my pdb
> file does not, but that's ok right?
>
> What is more, when I make a pdb file (savePDB file output.pdb) of
> the ligand, with leap after I loaded files using the first four
> lines in my leap.in file, that same pdb file cannot be reloaded back
> into leap without giving me the same error "20 atoms not is residue
> templates"
>
> I realize that I needed unique names for atoms in the past, but the
> prepin files had those unique names in them, while the mol2 does
> not. I think maybe this is where I am confusing the issue?
>
> Thanks, Steve
>
>
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]
> On Behalf Of case
> Sent: Wednesday, September 16, 2009 11:26 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] database
>
> On Wed, Sep 16, 2009, Steve Seibold wrote:
>
>> I have a mol2 file of a ligand which I have used to generate (using
>> parmchk) a ligand.frcmod file. So, I have the ligand.mol2 and
>> the ligand.frcmod. I changed the atom names of the ligand in my
>> protein/ligand complex pdb file so that the names are equivalent to
>> those found in the ligand.mol2 file.
>>
>> I am now trying to use the file.mol2 as a prepin file so that when
>> I load my protein/ligand complex I can generate topology and inpcrd
>> files.
>
> Here is the general tleap scheme:
>
> source leaprc.ff99SB (for example)
> source leaprc.gaff (to get the parameters needed for the ligand)
> loadAmberParams ligand.frcmod (to get the special parameters for
> your ligand)
> RES = loadMol2 ligand.mol2 (where "RES" is the name of the ligand residue)
> complex = loadPdb mycomplex.pdb (where this is the pdb file
> referred to above)
> saveAmberParm complex prmtop inpcrd
> quit
>
> Basically, the "loadMol2" command does for mol2 files what the
> "loadAmberPrep"
> file does for prepin files.
>
> ...hope this helps...dac
>
>
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>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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