VMD-L Mailing List
From: Diego Vazquez (dsvazquez86_at_gmail.com)
Date: Sun Aug 09 2015 - 00:59:17 CDT
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- In reply to: Neelanjana Sengupta: "writing initial coordinates in Amber format"
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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
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- In reply to: Neelanjana Sengupta: "writing initial coordinates in Amber format"
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