AMBER Archive (2002)

Subject: Re: mm pbsa: generate snapshots

From: Mathy Froeyen (Matheus.Froeyen_at_rega.kuleuven.ac.be)
Date: Thu Apr 18 2002 - 02:19:35 CDT

Dear Mark

I got the same error when running
mm_pbsa of amber release 70 on my trajectories.

I "patched" this problem
by using make_crd of amber release 6.0.

ie.
I created a soft link from the amber 7 exe directory
to the amber 6 directory

go to the directory amber7/exe/

mv make_crd_hg make_crd_hg.70
ln -s ../amber6/exe/make_crd make_crd_hg

It is not a clean solution, but in my case this worked.
My trajectories were generated using amber6 sander_classic.

regards,
mathy froeyen
----------------------------------------------
Mark Hsieh wrote:

> I tried to mimic the ras-raf example under
> $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots
>
> using a different protein-protein complex but I keep
> getting the error:
>
> =>> Creating coordinates
> Executing makecrd
> Box info found: 88.562 84.776 76.124
> Something wrong with NGR 3351 3350
> Broken pipe
>
> The box info corresponds to the box dimensions at the
> end of the first trajectory in the trajectory file.
>
> 3350 is the last atom of the receptor protein
> 3351 is the first atom of the ligand protein
>
> I can't seem to figure out why this does not work. I've
> tried removing the lines with the box dimensions and
> setting BOX option to "NO" but still get the same NGR
> message.
>
> Can someone tell me what I could be doing wrong?
>
> Thank you,
> Mark
>
> =======================================================
>
> My mm_pbsa.in file contains the section below:
> ----------------------------
> @MAKECRD
> BOX YES
> NTOTAL 47678
> NSTART 1
> NSTOP 5
> NFREQ 1
> NUMBER_LIG_GROUPS 1
> LSTART 3351
> LSTOP 5311
> NUMBER_REC_GROUPS 2
> RSTART 1
> RSTOP 1603
> RSTART 1604
> RSTOP 3350
> ----------------------------
> I've checked the numbers and numbering of the atoms and
> they seem correct.
>
> The protein-protein complex was initially solvated with Cl-
> ions and TIP3 (WATBOX216) in xleap.
>
> It was mininization and dynamics were done with sander
> using the input files below:
> ----------------------------
> minimization run
> &cntrl
> imin=1,
> maxcyc=100,
> ntpr=20,
> ntr=1,
> &end
> Restrain all atoms
> 10
> RESIDUE 1 14477
> END
> END
> ----------------------------
> molecular dynamics run
> &cntrl
> imin=0, irest=0,
> ntx=1,
> tempi=0.0, temp0=300.0,
> ntt=1, tautp=0.2,
> ntp=2, taup=0.2,
> ntb=2, ntc=2, ntf=2,
> nstlim=100,
> ntwe=20, ntwx=20, ntpr=20,
> &end
> ----------------------------