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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Received on Sat Nov 26 2011 - 11:30:04 PST
