Dear Dwight McGee,
The rec.out is following:
MM
GB
PB
MS
1
BOND = 1088.5783 ANGLE = 2923.9202 DIHED = 3933.3087
VDWAALS = -2898.3025 EEL = -24376.5504 HBOND = 0.0000
1-4 VDW = 1343.2510 1-4 EEL = 13052.3568 RESTRAINT = 0.0000
No error is given, and when I check the job (I ran in cluster, using
qstat to check the current job), it's still running, but no more file
is written within more than a day. It's very strange).
The input file for calculation is following:
################################################################################
.GENERAL
PREFIX DQ2.5-CLIP1
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./DQ2.5-CLIP1.prmtop
RECPT ./DQ2.5.prmtop
LIGPT ./CLIP1.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 0
GBSA 0
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
PROBE 0.0
#
#################################################################################
.PROGRAMS
################################################################################
I ran both AMBER 11 and 9. I also use IGB =2 and GBSA =2. But the
same problem I got.
You are right that I ran the Perl script, and I hadn't tried Python script.
Thank you for your time.
Best regards,
Nguyen Thanh Binh
PhD student, BII, Singapore
Quoting Dwight McGee <dwight.mcgee.gmail.com>:
> Hi,
>
> Could you provide us with a little more detail: 1) are there any error
> messages printed in the outputs files that you list in your previous email,
> 2) what is your input file and what version of AMBER are you using. Based
> on the naming of your output files I am assuming you are using the perl
> version MMPBSA. Do you get a similar error when you use MMPBSA.py (python
> version), it is available in AmberTools13, which is free to download?
>
>
> On Thu, Aug 1, 2013 at 10:29 PM, <nguyentb.bii.a-star.edu.sg> wrote:
>
>> Dear AMBER users,
>>
>> After getting 2000 snapshot from the MD trajectory, I want to
>> calculate both GPSA and PBSA for binding energy.
>> However, one of the snapshots, after giving me snapshot_com.out within
>> 1-2 minutes, it can't give full snapshot_rec.out up to 1-2 hours. The
>> calculation stops at surface area calculation and gives
>> snapshot_rec.pqr, snapshot_rec.pdb, snapshot_rec.mslog file.
>>
>> Could you please help me to solve this problem?
>> Thanks in advance.
>>
>> Regards,
>> Nguyen Thanh Binh
>> PhD student, BII, Singapore
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 01 2013 - 20:30:03 PDT
