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 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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>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Sep 19 2011 - 07:00:03 PDT
