oops, feel like I am talking too much. But after running pdb4amber, open
the file with _sslink ending, you will see
23 97
137 198
These are for S-S bond
bond x.23.SG <
http://x.23.sg/> x.97.SG <
http://x.97.sg/>
bond x.137.SG <
http://x.137.sg/> x.198.SG <
http://x.198.sg/>
<
http://x.198.sg/>Hai
On Sun, Nov 12, 2017 at 7:40 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>
> On Sun, Nov 12, 2017 at 7:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> hi
>>
>> the error message is here:
>>
>> WARNING: There is a bond of 6.744147 angstroms between:
>>
>> ------- .R<CYX 137>.A<CB 5> and .R<CYX 198>.A<O 10>
>>
>> This is a known bug in pdb4amber in AT17 that incorrectly write the
>> CONECT record.
>>
>> You can either
>> 1. delete the wrong CONECT record in the output pdb and explicitly create
>> the bond between S-S
>>
>> e.g: http://ambermd.org/tutorials/advanced/tutorial18/section1.htm
>>
>
> Example about this case:
> - Correct your HAC1.pdb by deleting 1st empty line
> - pdb4amber HAC1.pdb -o x.pdb
> - delete the incorrect CONECT lines in x.pdb
> - run tleap with below commands (just as an example)
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> x = loadpdb x.pdb
> bond x.23.SG x.97.SG
> bond x.137.SG x.198.SG
> set default PBradii mbondi3
> saveAmberParm x prmtop rst7
> quit
>
> Hai
>
>
>>
>>
>> 2. correct the CONECT field.
>>
>> PS: Other might have better experience about tleap.
>>
>> Hai
>>
>> On Sun, Nov 12, 2017 at 6:14 PM, jacky zhao <jackyzhao010.gmail.com>
>> wrote:
>>
>>>
>>> Hi
>>> Â We have used AT17 to generate the parm7 and crd files. The error
>>> message
>>> indicated that the CYX may not be recognized properly. I have
>>> attached the
>>> error message and pdb file below.
>>> However, the same pdb file can generate parm7 and crd files by using
>>> AT16.
>>> Anyone can give some suggestions?
>>> Thank you for taking your time.
>>> ååµå¾ç 1 Â
>>> --
>>> Lei Zhao, Ph.D.
>>> International Joint Cancer Institute of the Second Military Medical
>>> University
>>> National Engineering Research Center for Antibody Medicine
>>> New Library Building 11th floor,800 Xiang Yin Road
>>> Shanghai 200433
>>> P.R.China
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>
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Received on Sun Nov 12 2017 - 17:00:03 PST
