AMBER Archive (2008)

Subject: Re: AMBER: mmpbsa binding energy

From: Marc Lindner (nightfly21_at_gmx.de)
Date: Thu Jan 24 2008 - 04:16:23 CST

Thanks, Dr. Case for your advice. I guess the structures are OK.

But the next problem occured. In the archive I found an entry on 30.Okt.2006:

Varsha Goyal wrote:

>Thanks Angelo,
>It solved my problem but now when I am running
>binding_energy.mmpbsa evertime it causes some problem
>with my ligand file.
>Error looks like this:
>
>/usr/local/amber8/exe/pbsa -O -i pbsa.in -o
>pbsa_lig.1.out -c ./extract_coord/snapshot_lig.crd.1
>-p ./prmtop.ets not successful
>
>I am not sure where should I look because when I look
>at the structure for this trajectory in VMd it looks
>fine to me.
>Can you or someone else please suggest solution to
>this problem?
>
>Thanks in advance,
>Varsha

I have the same problem with the calculation of the snapshots. I splitted the snapshots in each nanosecond. And calculated the Enthalpie with mm_pbsa.pl. This works for the first and second nanosecond, but the 10th lig_snapshot in third and the first lig_snapshot in fourth nanosecond MD abort with previous given error. I checked my input. Topology file is OK. I can create pdb from Y.prmtop and snapshot_lig.crd.1. The path is correct. Can anyone help me with this mistake. In snapshots_lig.all.out the line corrected reaction field energy is missing for these ligands.

Thanks in advance,
Marc

P.S.: Here my input:

extract_coords.mmpbsa:
@GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./Z.prmtop
RECPT ./X.prmtop
LIGPT ./Y.prmtop
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
@MAKECRD
BOX YES
NTOTAL 44536
NSTART 1
NSTOP 100
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 3969
LSTOP 4001
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3969
@TRAJECTORY
TRAJECTORY ./prod1.mdcrd
TRAJECTORY ./prod2.mdcrd
@PROGRAMS

binding_energy.mmpbsa:
@GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ../Z.prmtop
RECPT ../X.prmtop
LIGPT ../Y.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
@MM
DIELC 1.0
@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
@MS
PROBE 0.0
@PROGRAMS

-------- Original-Nachricht --------
> Datum: Wed, 23 Jan 2008 08:24:15 -0800
> Von: "David A. Case" <case_at_scripps.edu>
> An: amber_at_scripps.edu
> Betreff: Re: AMBER: distorted aromatic rings

> On Wed, Jan 23, 2008, Marc Lindner wrote:
>
> > I have problems to keep aromatic rings flat. Using the forcefields 99SB
> and
> > 03 all aromatic rings of the protein and the ligand get distorted. The
> input
> > preparation with antechamber (gaff) for the ligand and with xleap/ff03
> for
> > the protein causes no warnings for bonds, angels and torsions (just few
> > close contacts in the protein and a non-zero charge). While
> saveamberparm
> > the message appears: total 15 improper torsions applied (ligand); total
> 799
> > improper torsions applied (protein).
>
> How non-planar are they? You can visually see distortions in MD
> simulations,
> since only the average structure is truly planar. So, it's not clear
> whether
> you are seeing something that is incorrect, or just something that is
> surprising.
>
> ...dac
>
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