[gmx-users] g_sas problem?

[Justin Lemkul]

On 1/6/15 2:33 AM, Albert wrote:
> Thanks a lot for the reply.
>
> I believe this 122 atoms belong to my ligand. I generate the ligand.itp file by
> acpype tool and the system was assigned for Amber FF.
>
> BTW, why does g_sas ask twice to select a group for output as following?
>

Read the help description.

-Justin

> and a group for output:
> Select a group: 26
> Selected 26: 'Protein_UNK'
> Select a group: 26
> Selected 26: 'Protein_UNK'
>
> Thanks again.
>
> Albert
>
>
> On 01/06/2015 12:14 AM, Justin Lemkul wrote:
>> Well, clue #1:
>>
>> WARNING: could not find a Van der Waals radius for 122 atoms
>>
>> You've got something in the system that isn't covered by vdwradii.dat; find
>> out what that is and you'll start to diagnose the issue.
>>
>> -Justin
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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