Indeed. I did so.
That's why I'm baffled by the error message. Furthermore, tleap did not issue error messages when I saved the protein and complex prmtop files. It complained only when I tried to save the solvated complex topology file.
Best regards
George
Sent from my iPhone
On 26 Nov 2011, at 21:36, Yong Duan <duan.ucdavis.edu> wrote:
>
> Did you re-name the corresponding CYS to CYX?
>
> --
> Yong Duan, Ph.D, Professor
> UC Davis Genome Center and
> Department of Biomedical Engineering
> University of California at Davis
> Davis, CA 95616
> 530-754-7632
>
>
>
>
>
>
> On 11/26/11 11:10 AM, "George Tzotzos" <gtzotzos.me.com> wrote:
>
>> Just to clarify my earlier message.
>>
>> The complex.pdb file that I submitted to tleap did NOT have connect
>> records. So the error message is perplexing.
>>
>> Which leads me to ask the following question.
>>
>> If CONNECT records are included in the the submitted pdb file, does this
>> mean that it is not necessary to issue an explicit bond command? This is
>> not clear in the Amber 11 manual.
>>
>> Thanks in advance for the advice
>>
>> George
>>
>>
>> On Nov 26, 2011, at 7:13 PM, George Tzotzos wrote:
>>
>>> Hi everybody,
>>>
>>> I'm repeating the preparation of topology files for a ligand-receptor
>>> complex.
>>>
>>> The files have been prepared without tleap issuing any untoward
>>> warnings.
>>>
>>> On solvating the system, I got
>>>
>>>> saveamberparm COMPLEX 2erb_indole_solv.prmtop 2erb_indole_solv.inpcrd
>>> Checking Unit.
>>> Building topology.
>>> Building atom parameters.
>>> Building bond parameters.
>>> Building angle parameters.
>>> Building proper torsion parameters.
>>> !FATAL ERROR----------------------------------------
>>> !FATAL: In file [unitio.c], line 1788
>>> !FATAL: Message: 1-4: cannot add bond 386 874
>>> This may be caused by duplicate bond specifications;
>>> for example, explicit bond commands in addition to PDB conect records.
>>> !
>>> !ABORTING.
>>>
>>> I'm rather stuck. Your advice how to overcome this problem would be
>>> most welcome.
>>>
>>> As I mentioned this is a repeat prep. On earlier occasions I didn't get
>>> anything like this. The only thing that I did differently this time was
>>> to construct 3 disulfice bonds issuing the commands:
>>>
>>> COMPLEX=loadpdb 2erb_indole.pdb
>>>> bond COMPLEX.26.SG COMPLEX.57.SG
>>>> bond COMPLEX.53.SG COMPLEX.104.SG
>>>> bond COMPLEX.95.SG COMPLEX.113.SG
>>>
>>> saveamberparm COMPLEX 2erb_indole.prmtop 2erb_indole.inpcrd
>>>
>>> and the same for the receptor.
>>>
>>> Best regards
>>>
>>> George
>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Nov 26 2011 - 14:00:02 PST
