AMBER Archive (2008)

Subject: Re: AMBER: xleap fails to savemol2

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Aug 28 2008 - 23:58:08 CDT

Quoting taufik.alsarraj_at_utoronto.ca:

> i have a mol2 file, i can read it just fine with xleap and i can also
> convert it to *.prmtop and *.inpcrd. However i cannot savemol2.
>
> my script:
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberparams mysioforce.frcmod
> sur = loadmol2 "newsurface.mol2"
> check sur
> saveamberparm surfacealone.prmtop surfacealone.inpcrd
> savepdb sur surface.pdb
> savemol2 sur surface0.mol2 0
> savemol2 sur surface1.mol2 1
> solvatebox sur TIP3PBOX 8.0
> saveamberparm surfacesolvent.prmtop surfacesolvent.inpcrd
> edit sur
>
> i attached mysioforce.frcmod and newsurface.mol2
> savepdb fails and savemol2 (0 and 1) causes xleap to crash.
>
> Any suggestions?,

I did not test with Amber10 yet, but with Amber8 + source files
available from http://q4md-forcefieldtools.org/Tutorial/leap.php.

I am not sure your Tripos mol2 file format is correct in your input structure.
See the official description of this file format:
http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
& for a simple example, see:
http://q4md-forcefieldtools.org/REDDB/up/W-1/tripos1.mol2

In particular in your mol2 file:
1) the "number of residue" is not present:
890 970
=>
890 970 1 0 1

2) the "substructure" information is empty:
=> add at the end of your file such a line:
       1 UNK 1 **** 0 **** ****

Does it help ?

regards, Francois

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