AMBER Archive (2008)

Subject: Re: AMBER: xleap fails to savemol2

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 04 2008 - 14:45:49 CDT

Quoting taufik.alsarraj_at_utoronto.ca:

We just compiled Ambertools 1.2 + Amber 10 on CentOS release 5.2
The "savemol2" (xleap & tleap) command works fine.

May I ask you the operating system + machine + compilers used to
install the Ambertools 1.2 ?

regards, Francois

> Yes xleap crashes
> out put has one line in the atoms only
> @<TRIPOS>MOLECULE
> DMSO
> 10 9 1 0 1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
> 1 C1 1.352237 -0.856933 0.225852 C 1 DMSO
> -0.2897 *
> ***
>
> --that is the end of tripos2.mol2
>
>
> Quoting FyD <fyd_at_q4md-forcefieldtools.org>:
>
>> Quoting taufik.alsarraj_at_utoronto.ca:
>>
>>> Thank you for the suggestions. Unfortunately xleap and tlean still
>>> crashes.
>>
>> We will have Amber10 installed pretty soon: We will test this...
>>
>> Using the more basic Tripos mol2 file available @
>> http://q4md-forcefieldtools.org/REDDB/up/W-1/tripos1.mol2
>> may I ask you to run this simple script:
>>
>> TEST = loadmol2 tripos1.mol2
>> savemol2 TEST tripos2.mol2 0
>>
>> Does it crash also ?
>>
>> regards, Francois

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