[gmx-users] 11-cis retinal topology problem

[Justin Lemkul]

On 7/6/13 4:17 PM, Mark Abraham wrote:
> On Sat, Jul 6, 2013 at 4:30 PM, Albert <mailmd2011 at gmail.com> wrote:
>> On 07/06/2013 12:14 PM, Mark Abraham wrote:
>>>
>>> My bad. Use
>>>
>>> warning_note(wi, "Debugging");
>>
>>
>>
>> thanks a lot Mark. I've obtained some informations now:
>
> That's a completely different output. I think both your executables
> are broken, somehow. Clean the build and install trees and try again
> :-)
>
> Mark
>
>> Identified residue MET1 as a starting terminus.
>> Warning: Residue RETK296 in chain has different type (Other) from starting
>> residue MET1 (Protein).
>> Warning: Residue THR297 in chain has different type (Protein) from starting
>> residue MET1 (Protein).
>> Warning: Residue SER298 in chain has different type (Protein) from starting
>> residue MET1 (Protein).
>> Warning: Residue ALA299 in chain has different type (Protein) from starting
>> residue MET1 (Protein).
>> Warning: Residue VAL300 in chain has different type (Protein) from starting
>> residue MET1 (Protein).
>> More than 5 unidentified residues at end of chain - disabling further
>> warnings.
>> Identified residue ALA295 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>> Fatal error:
>> Residue 1 named LEU of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom N used in
>> an interaction of type improper in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.

This problem can be solved by remembering to complete step 5 of 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.

As Mark notes, though, this issue is entirely separate from your initial problem.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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