Re: [AMBER] Using tleap tho have the .inpcrd and crd file

From: ABEL Stephane <>
Date: Thu, 30 Apr 2020 14:16:53 +0000

Thank your Pr Case it is worked


De : David A Case []
Envoyé : mercredi 29 avril 2020 13:20
À : AMBER Mailing List
Objet : Re: [AMBER] Using tleap tho have the .inpcrd and crd file

On Tue, Apr 28, 2020, ABEL Stephane wrote:
>I would like to use tleap to obtain the corresponding .inpcrd and crd
>files from a PDB of a solvated system that contains X molecules of
>Glycolipids and Y waters obtained from a previous MD with GROMACS
>I have already the mol2/prmtop files for one glycolipid molecule based on
>GLYCAM06 and the water is the tip3p water model obtained with tleap. I
>did not find a tutorial to explain to how to do.

First, make a single PDB file that has everything you want (or that you
had in gromacs.) Put TER cards between glycolipid molecules if they are
not already there.

Second, run tleap: load the mol2 files, the leaprc.water.tip3p, any
other units you will need. Then use loadPdb to load your pdb. If you
pdb file was from a periodic simulation, then use

    set x box { 32.5 50.0 37.8}

where "x" is the name you gave in the loadPdb command, and the numbers
are the box lengths. (If you have a non-rectangular box, you will have
to learn how to use ChgBox.)

Be sure to visualize the system, check visually that the bounding box is
in the correct place, check the initial structure for bad contacts, etc.

...hope this helps....dac

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