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 1.5, 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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Received on Sun Sep 18 2011 - 23:30:02 PDT
