I'm using mm, gb, pb and ms... This is my input:
.GENERAL
PREFIX snapshot_DNA_TD22_2
PATH ../extract_coords-II
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../DNA_TD22_2_bv.top
RECPT ../DNAzaTD22_2_bv.top
LIGPT ../TD22_2_bv.top
#
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
#
PB_SURFTEN 0.0072
PB_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
#
Citiram Dwight McGee <dwight.mcgee.gmail.com>:
> Which function of mm_pbsa.pl are you using, for example, gb, pb?
>
> On Thu, Feb 11, 2010 at 9:51 AM, Marina Grabar <Marina.Grabar.irb.hr> wrote:
>
>> Hello,
>>
>> I'm trying to calculate free energies of binding (for complex between DNA
>> and small molecule) with MM_PBSA method. I run the following command: "
>> mm_pbsa.pl mm_pbsa_Binding.in > mm_pbsa_Binding.log" and after few minutes
>> I got the message: "No data for 0+1 MM BOND 480". In my new log file there
>> is no final part for statistics. I also tried to run
>> mm_pbsa_statistics.pl(because it produced three intermediate files:
>> snapshot_DNA_TD22_2_com.all.out, snapshot_DNA_TD22_2_rec.all.out and
>> snapshot_DNA_TD22_2_lig.all.out) but after running it I became:
>> =>> Reading input
>> =>> Reordering files
>> Final order:
>> 1. snapshot_DNA_TD22_2_com.all.out: -
>> 2. snapshot_DNA_TD22_2_rec.all.out: -
>> 3. snapshot_DNA_TD22_2_lig.all.out: -
>> =>> Reading files
>> =>> Values of parameters
>> TEMP = 300
>> R = 8.314
>> =>> Treat special parameters
>> =>> Calc missing parameters
>> =>> Calc average and stddev
>> =>> Print output (decomp) to snapshot_DNA_TD22_2_statistics.out
>> snapshot_DNA_TD22_2_statistics.out not opened
>>
>> ...and, of course, no statistics output file.
>>
>> Btw, we installed Amber 10 just few days ago and patched the latest version
>> of bug fixes.
>>
>> I would be very grateful if anyone could help me to fix this problem...
>>
>> Best regards,
>> Marina
>>
>> --
>> Marina Grabar, B.Sc.
>> Institute Rudjer Boskovic
>> Bijenicka 54
>> HR-10000, Zagreb
>> CROATIA
>> tel +385-1-4561025
>> fax +385-1-4680245
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Marina Grabar, B.Sc.
Institute Rudjer Boskovic
Bijenicka 54
HR-10000, Zagreb
CROATIA
tel +385-1-4561025
fax +385-1-4680245
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Received on Thu Feb 11 2010 - 07:30:03 PST
