Dear amber users：
I am running MM-PBSA module with following ptraj input file to genetare mdcrd file for snapshots.
trajin ./md3.mdcrd
strip :192-11805
trajout ./md3.trj nobox time 2
I am trying to calculate the binding free energy of my receptor - ligand complex (both are protein chains) using MM-PB(GB)SA. When I run the mm_pbsa script I eventually get the results(statistics.out etc.), however I also get this message too,
vertex atom mismatch
atom: 2825
vertex atom: 2823
my input file is mmpbsa.in ，this is
.GENERAL
PREFIX 1i8a
PATH ./crd
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./comp.prmtop
RECPT ./pro.prmtop
LIGPT ./lig.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 0.00
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 0.05
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.0
.MS
PROBE 0.0
.PROGRAMS
I searched the list but I could not figure out the problem. Anybody have an idea?
Also I want to ask a second question,
Before extracting the snapshots from the explicit water trajectory for this calculation, do we have to strip away the waters and ions with ptraj? (I mean we already define where the receptor and ligand starts and ends in the script) If we do not, does this effect the final results?
Thanks for the help.
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Received on Tue Sep 09 2014 - 06:00:02 PDT
