Hello again,
It is really strange the benzene ring in the pdb file extracted from the trajectory is not coplanar but twisty. Also, it is not shown in aromatic way.
> On Mar 15, 2019, at 4:37 PM, Zhonghua Xia <zhonghua.xia.helmholtz-muenchen.de> wrote:
>
> Dear Bill and David,
>
> I appreciate your kind help!
>
> Actually I went back to see the mol2 file. Then I found that antechamber cannot identify aromatic bond. When I use antechamber to convert pdb to mol2 for the ligand, it just converts every connection to single bond.
>
> Also, I found antechamber and tleap cannot identify chlorine atom. I tried to manually change notation of chlorine to CL, cl or Cl in the mol2 file and pdb file generated by pdb4amber. No matter which way I use, finally I can’t get the molecule correctly with chlorine atom as shown by MOE and pymol.
>
> Could you give me any help on this?
>
> Kind regards,
> Zhonghua
>
>> On Mar 8, 2019, at 3:13 PM, David A Case <david.case.rutgers.edu> wrote:
>>
>> On Fri, Mar 08, 2019, Zhonghua Xia wrote:
>>
>>> Initial minimisation with Cartesian restrains for the solvent (hold the protein and Cl-)
>>> &cntrl
>>> imin=1, maxcyc=3000,
>>> ntr=1,
>>> restraint_wt=100,
>>> restraintmask=':1-90'
>>> &end
>>
>> Set ntpr=1 to get more detailed output. Also, you can use the "check"
>> command in cpptraj to analyze your system for bad contacts.
>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 1 4.3472E+08 2.4011E+02 1.9793E+04 C 1441
>>>
>>> BOND = 9784.2491 ANGLE = 1786.4015 DIHED = 934.9579
>>> VDWAALS = ************* EEL = -62579.0562 HBOND = 0.0000
>>> 1-4 VDW = 1083.6816 1-4 EEL = 4202.4250 RESTRAINT = 0.0000
>>
>> Still, it's a bit unusual that an initial energy of "only" 4 x 10^8
>> won't minimize away. Try reducing your restraint weight by at least a
>> factor of 10. If the bad contact is in residues 1-90, then your
>> powerful restraints are forcing those atoms to stay where they are.
>> Hence you may have to two very strong and competing energy terms, one
>> trying to relieve a bond contact and another trying to keep it in place.
>>
>> ...good luck...dac
>>
>>
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Received on Fri Mar 15 2019 - 10:00:03 PDT
