Dear mish and Lyachele:
Thanks for your reply and suggestions. I used AmberTools1.5 and amber11 for the previous calculations. As your instructions, I recompiled Ambertools1.5 with the newest patch and used tleap instead.
However, the DIHED energy still varies a lot. If I source ff99SB first, DIHED of complex with ff99SB and Glycam06 is still 5xxx and the apo protein with ff99SB is 11xxx.
Furthermore, the different orders of source ff still influence the numbers of DIHED force constants in the topology files and the DIHED energy in the output files.
I checked the 2 top files of the complex from different source ff order, and compared them with top files of apo protein and ligand only. I found that if I source ff99SB and then Glycam06, I would get 3 more DIHEDRAL FORCE CONSTANT in the complex top file. ( but there is no covalent bond between the glycan and protein) So dose that mean if I have a protein with glycan, I have to source Glycam06 first and then ff99SB? Or these two forcefield have something overlap?
Ken
Here are the output files
-----------------------------------------------------------------------------------------
source ff99SB and then Glycam06 in tleap (with the same process, but I dont know why it has one more water than the later one)
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.5801E+05 1.3754E+01 8.8330E+02 O 12169
BOND = 1910.1638 ANGLE = 5851.0122 DIHED = 5336.5558
VDWAALS = 50000.1349 EEL = -578511.1926 HBOND = 0.0000
1-4 VDW = 6490.3105 1-4 EEL = 50916.8409 RESTRAINT = 0.0000
------------------------------------------------------------------------------------------
source Glycam06 and then ff99SB in tleap
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.4787E+05 1.3761E+01 8.8258E+02 O 12169
BOND = 1910.1638 ANGLE = 5867.8126 DIHED = 11546.5681
VDWAALS = 50051.2635 EEL = -578496.9408 HBOND = 0.0000
1-4 VDW = 6500.8097 1-4 EEL = 54755.1697 RESTRAINT = 0.0000
------------------------------------------------------------------------------------------
在 2011/9/19 的來信中，"Lachele Foley (Lists)" <lf.list.gmail.com> 提及：
>You have to use a patched AT 1.5, and use *tleap* not sleap.
>
>
>On Mon, Sep 19, 2011 at 2:15 AM, mish <smncbr.gmail.com> wrote:
>> Dear Ken:
>>
>> Which version of AmberTools you are using ?? There was a bug in sleap which
>> has been patched few months back. You can have a look:
>> http://archive.ambermd.org/201103/0307.html
>> Have you tried to compare parm file created by both ways ??
>>
>> ..mish
>>
>> On Mon, Sep 19, 2011 at 7:50 AM, <d944286.oz.nthu.edu.tw> wrote:
>>
>>> Dear amber users:
>>>
>>> My system consists of a dimer-protein and one sugar in 10A water box, and
>>> the sugar dosent has any covalent bond with the protein. I met a problem of
>>> huge different DIHED when I tried to use MMPBSA to calculate the free energy
>>> though single or triple trajectories. DIHED of complex is 5xxx and the
>>> protein is 11xxx. (the other energy terms look fine)
>>>
>>> So I went back to check my procedures of preparing the system and tried to
>>> find some information from the mail list and FAQ. Some people mantioned that
>>> the different scaling factor may cause the energy variation. But as David
>>> Case and Rose walker said, in Amber11 and Ambertool 15, sander would assign
>>> the scaling factor (scee=1.2,scnb=2.0) automatically.
>>>
>>> In my output file, it showed the information below.
>>>
>>>
>>> --------------------------------------------------------------------------------------
>>> | Note: 1-4 EEL scale factors were NOT found in the topology file.
>>> | ? ? ? Using default value of 1.2.
>>>
>>> | Note: 1-4 VDW scale factors were NOT found in the topology file.
>>> | ? ? ? Using default value of 2.0.
>>>
>>> --------------------------------------------------------------------------------------
>>>
>>> So I think the different DIHED may not be attributed to the scaling factor.
>>>
>>> Another possibility of the different DIHED may be the overlap of the
>>> Glycam06 and ff99SB. I checked the parameter files of these two ff and I
>>> found that only one atom type "Cy" has different difinetions in these two
>>> ff. One is sp2 and the other one is sp3. But both my complex and protein
>>> dont have the atom type "Cy". So I think the overlapping atom type "Cy" may
>>> not casue the different DIHED neither.
>>>
>>> When I checked my procedures of preparing the system and tried different
>>> source ff order to generate my top and rst file. I found something strange.
>>> If I source ff99SB first and then source Glycam_06, the DIHED of complex
>>> became 5xxx. But if I source Glycam_06 first and then ff99SB, it became
>>> 11xxx !!
>>>
>>> Although my apo protein system comprises no glycan, I tried this in my apo
>>> protein too. If I source only ff99SB, the DIHED was 11xxx. If I source
>>> ff99SB first and then Glycam_06, the DIHED was 5xxx. But if I source
>>> Glycam_06 first and then ff99SB, it became 11xxx again.
>>>
>>> In both apo and complex, the DIHED 11xxx looks more appropriate, because my
>>> dimer-protein comprises almost 1000 residues But I still wonder what causes
>>> this different DIHED and ensure there is nothing inappropriate for my later
>>> mmpbsa calculation.
>>>
>>> Best regards :)
>>> Ken
>>>
>>>
>>> --------------------------------------------------------------------------------------
>>> These are my operation steps in sleap
>>>
>>> source leaprc.ff99SB
>>> source leaprc.Glycam_06
>>> com = loadpdb xxx.pdb
>>> addions com 38 Na+ 12 Cl-
>>> solvatebox com TIP3PBOX 10.0
>>> saveamberparm com xxx.top xxx.rst
>>>
>>>
>>> --------------------------------------------------------------------------------------
>>> Here is my input file of min Complex.
>>>
>>> minimise
>>> ?&cntrl
>>> ?imin=1,maxcyc=1000,ncyc=500,
>>> ?cut=10.0,ntb=1,
>>> ?ntpr=100,
>>> ?ntr=1, restraintmask=':1-1114.CA,C,N',
>>> ?restraint_wt=5.0
>>> ?nmropt=1,
>>> ?&end
>>> ?&end
>>> ?&wt type='END'
>>> ?&end
>>> ?DISANG=dist.rst
>>>
>>>
>>> -------------------------------------------------------------------------------------
>>> Output file 1 (source Glycam_06 and then ff99SB)
>>>
>>> ? ? ? ? ? ? ? ? ? ?FINAL RESULTS
>>>
>>>
>>> ? NSTEP ? ? ? ENERGY ? ? ? ? ?RMS ? ? ? ? ? ?GMAX ? ? ? ? NAME ? ?NUMBER
>>> ? 1000 ? ? ?-4.9221E+05 ? ? 4.9197E-01 ? ? 4.8894E+01 ? ? CE1 ? ? ?4127
>>>
>>> ?BOND ? ?= ? ?33940.8786 ?ANGLE ? = ? ? 2723.5512 ?DIHED ? ? ?=
>>> 4600.0170
>>> ?VDWAALS = ? ?70077.5842 ?EEL ? ? = ?-661208.6465 ?HBOND ? ? ?=
>>> ?0.0000
>>> ?1-4 VDW = ? ? 4062.8436 1-4 EEL = ? ?52654.8763 ?RESTRAINT ?=
>>> ?936.5455
>>> ?EAMBER ?= ?-493148.8955
>>> ?NMR restraints: Bond = ? ?1.869 ? Angle = ? ? 0.000 ? Torsion = ? ? 0.000
>>>
>>>
>>> ----------------------------------------------------------------------------------------
>>> Output file 2 (source ff99SB and then Glycam_06)
>>>
>>> ? ? ? ? ? ? ? ? ? ?FINAL RESULTS
>>>
>>>
>>> ? NSTEP ? ? ? ENERGY ? ? ? ? ?RMS ? ? ? ? ? ?GMAX ? ? ? ? NAME ? ?NUMBER
>>> ? 1000 ? ? ?-5.2555E+05 ? ? 4.2406E-01 ? ? 4.0278E+01 ? ? CD ? ? ?14860
>>>
>>> ?BOND ? ?= ? ?37003.3845 ?ANGLE ? = ? ? 2663.2636 ?DIHED ? ? ?=
>>> ?10799.4054
>>> ?VDWAALS = ? ?77597.0227 ?EEL ? ? = ?-711210.8832 ?HBOND ? ? ?=
>>> ?0.0000
>>> ?1-4 VDW = ? ? 4054.2862 1-4 EEL = ? ?52593.7994 ?RESTRAINT ?=
>>> ?947.6604
>>> ?EAMBER ?= ?-526499.7214
>>> ?NMR restraints: Bond = ? ?1.686 ? Angle = ? ? 0.000 ? Torsion = ? ? 0.000
>>>
>>>
>>> ---------------------------------------------------------------------------------------
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>
>
>
>--
>:-) Lachele
>Lachele Foley
>CCRC/UGA
>Athens, GA USA
>
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Received on Tue Sep 20 2011 - 09:00:02 PDT
