AMBER Archive (2009)

Subject: Re: [AMBER] problem with FAD in tleap

From: M. Shahid (mohammad.shahid_at_gmail.com)
Date: Mon Nov 30 2009 - 12:33:35 CST

Hi,

On Mon, Nov 30, 2009 at 6:15 PM, case <case_at_biomaps.rutgers.edu> wrote:

> On Mon, Nov 30, 2009, M. Shahid wrote:
>
> > then tleap went find and got no complaints
>
> Good.
>

Were those parameters correct?

>
> > but at the end converting topology to pdb by ambpdb was not working.
> >
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line
> > Source
> > ambpdb 0804FBA4 Unknown Unknown Unknown
> > ambpdb 0804A1C5 Unknown Unknown Unknown
> > ambpdb 08048222 Unknown Unknown Unknown
> > ambpdb 080B15A2 Unknown Unknown Unknown
> > ambpdb 08048101 Unknown Unknown Unknown
> >
> >
> > I guess I used the wrong parameters.
>
> The fact that ambpdb failed probably has nothing to do with what parameters
> you used. We would need to know if ambpdb works for other prmtop files,
> what
> compiler and OS (and amber version) you used, and so on.
>
> I am using SL x86_64 with g77 and had compiled correctly AmberTools1.0 with
bugfix.all patch.
Yes, the ambpdb worked previously on other prmtop files but started this
problem
when I used the new parameters in parm99.dat and created prmtop/crd files
with tleap.

> >
> > I also tried to use FAD params from
> > http://www.pharmacy.manchester.ac.uk/bryce/amber
> > but also doesn't work in my case.
>
> Hard to be of much help without more information. Just saying "doesn't
> work"
> is of no help when trying to debug something remotely.
>

Sorry for that, as I am using leaprc.ff99SB with parm99 and that one using:
PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy
progs

and I get no errors when I use it with FAD.mol2
but the problem I am facing now with ambpdb

I also checked on just fad and there is a strange character 'Y' in the
output pdb:

-bash-3.2$ ambpdb -p fad.top < fad.crd

| New format PARM file being parsed.
| Version = 1.000 Date = 11/30/09 Time = 19:27:07
REMARK
ATOM 0 Y FAD 4 0.000 0.000 0.000
ATOM 1 O3B FAD 4 58.127 139.363 12.551
ATOM 2 H3T FAD 4 58.026 140.041 11.896
ATOM 3 C1B FAD 4 56.137 136.961 12.309
.............the rest is ok.

Best regards, 

--
Shahid.

> ...dac
>
>
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