[gmx-users] 11-cis retinal topology problem

Justin Lemkul jalemkul at vt.edu
Sun Jul 7 03:18:42 CEST 2013



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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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