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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Sun Nov 12 2017 - 17:00:02 PST
