Sorry, in my previous message
It should be .<TRIPOS>BOND records instead of the "CONECT" records
Stephane
________________________________________
De : ABEL Stephane 175950
Date d'envoi : mercredi 22 mai 2013 15:26
À : AMBER Mailing List
Objet : [PROVENANCE INTERNET] [AMBER] RE : How to construct a mol2 file from a PDB and RESP outputfiles ?
Hello Pr Case,
Thank you for your response.
As I said in my previous message, It is possible to obtain mol2 file from a PDB with CHIMERA (for example), but this mol2 file will not contain in the last column the computed RESP.
So I have also tried antechamber, but it is not clear to me which file i need to obtain in the mol2 file
- the coordinates of the optimized geometry of my molecule
- the "CONECT" records
- the RESP charges.
It is possible to do that with antechamber ?
Stephane
_______________________________________
De : David A Case [case.biomaps.rutgers.edu]
Date d'envoi : mercredi 22 mai 2013 15:08
À : AMBER Mailing List
Objet : Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ?
On Wed, May 22, 2013, ABEL Stephane 175950 wrote:
>
> It is possible to generate a mol2, if I have only a PDB of my molecule
> and a file generated by the RESP program. If yes, how ?
If you want to use the mol2 for futher work in Amber, look at the antechamber
program.
If you plan to use the mol2 file for other purposes, many programs can help,
including chimera, as already mentioned here.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 22 2013 - 07:00:03 PDT
