VMD-L Mailing List

From: Diego Vazquez (dsvazquez86_at_gmail.com)
Date: Sun Aug 09 2015 - 00:59:17 CDT

Dear Neelanjana,

If you already have the pdb files, you can easily create the .inpcrd files
using tleap by something like this:

source leaprc.ff14SB
loadamberparams frcmod.ionsjc_tip3p

mol = loadpdb XXXX.pdb
addIons2 mol Na+ 0
solvateOct mol TIP4PBOX 12
saveAmberParm mol yourfile.inpcrd
quit

On 8 August 2015 at 03:40, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:

> Dear All,
>
> For a given system, I have the Amber topology/parameter (or .prmtop) and
> coords (.inpcrd) file. However, I wish to start some runs for this system
> with a slightly different initial coordinates, for which I have .xyz / .pdb
> files. VMD loads the new .xyz with the .prmtop.
>
> Can VMD write out the new coordinates in .incprd format? Some pointers
> would be helpful.
>
> Thanks in advance,
> Neelanjana
>
> 

-- 
**************************************************
Lic. Diego Sebastian Vazquez
Laboratorio de Biofísica de Proteínas
IQUIFIB - Departamento de Química Biológica
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires, Argentina
Junín 956 (1113)
Tel: (+54 11) 4964-8289 int. 108
dsv_at_qb.ffyb.uba.ar