> On Mar 4, 2015, at 2:49 AM, Atila Petrosian <atila.petrosian.gmail.com> wrote:
>
> Dear amber users
>
> I am doing MM-PBSA calculation for my protein-ligand system based on TUTORIAL
> A3: MM-PBSA <http://ambermd.org/tutorials/advanced/tutorial3/index.htm>
> using AmberTools 14.
>
> I encountered a problem in section 3 of this tutorial:
>
> http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
>
> After successfully extracting of snapshots, I prepared input file (
> binding_energy.mmpbsa).
> --------------------------------------------------------------------------------------------------
> .GENERAL
> VERBOSE 0
> PARALLEL 0
> PREFIX snapshot
> PATH ./
> START 200
> STOP 300
> OFFSET 1
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./comp1.prmtop
> RECPT ./hsa1.prmtop
> LIGPT ./sal1_h.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 1
> MS 1
> NM 1
> .PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 5
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> ARCRES 0.0625
> INP 1
> SURFTEN 0.005
> SURFOFF 0.00
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> .MM
> DIELC 1.0
> .GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> SURFTEN 0.005
> SURFOFF 0.00
> .MS
> PROBE 0.0
> .NM
> DIELC 4
> MAXCYC 1000
> DRMS 0.1
> .PROGRAMS
> --------------------------------------------------------------------------------------------------
> Then I used this command:
>
> $AMBERHOME/bin/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> But I get following:
>
> Param PROC does not exist
> For details see:
> http://ambermd.org/Questions/mm_pbsa.html#testpar_param_not_existent
>
> How to resolve this problem?
Maybe you need to add the PROC keyword to the NM section? See the manual for details. If that doesn’t work, I would suggest trying MMPBSA.py instead (also in Tutorial 3). That version is typically better-supported on the mailing list.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 04 2015 - 05:00:02 PST
