AMBER Archive (2009)

Subject: Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Fri Jul 31 2009 - 20:39:54 CDT

First of all i believe you should use leaprc.ff03
Then if the errors are there regarding definitions, save them in the
atom94.lib using redirectional operator ">".
Now load it again.
Remember that your file doesnt have definitions required for the structure.
Regards
Ashish Runthala

On Fri, Jul 31, 2009 at 11:06 PM, Brothers, Michael
Charles<mcbroth_at_sandia.gov> wrote:
> Thanks Ashish
>
> I think I fixed the problem by using the remove bond command (although I'm having issues with the syntax to remove the atoms themselves...hoping this won't be a problem.
>
> Only problem now is that when I try to save it as a .prmtop file it can't find its type.  I tried modifying the leaprc.ff99SB file to include the new atom hybridizations (ex:  { "N3" "n" "sp3" }, see attached) but for some reason when I have it in my home directory it won't load properly, rendering my patch useless.
>
> Does the forcefield file have to be in the cmd directory?  If it doesn't, am I missing something, as my new forcefield file will not load properly.
>
> Thanks,
>
> Mike
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of Ashish Runthala
> Sent: Thursday, July 30, 2009 8:41 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR
>
> See
> you used solvatecap which has made an array but the velocities are assigned zero in all three directions of the velocity vector(0,0,0) And hence the sander being smart enough halts the script saying a segmentation fault.
> Just check your pdb file again, making its confirmation detail proper to be used for the sander.
>
> On Fri, Jul 31, 2009 at 7:28 AM, Brothers, Michael Charles<mcbroth_at_sandia.gov> wrote:
>> Dear Amber Users,
>>
>> I attached my original PDB file (33GMBS.pdb), my modified .oFF file from RED with protecting groups, my modified .oFF file from RED without protecting groups, and the PDB file that resulted (A.pdb).
>>
>> I have the following errors:
>>
>> 1)  If I use my .oFF file with the protecting groups, it reinserts
>> them automatically (GMBSX.off)
>>
>> 2)  If I use my .oFF file with the protecting groups removed
>> (manually), it claims that there is a segmentation fault and shuts
>> down the program (GMBS.off)
>>
>> Any ideas/suggestions?
>>
>> Thanks,
>>
>> Mike
>>
>>
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>>
>
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Lecturer, Biological Sciences,
> Birla Institute of Technology and Science, Pilani, Rajasthan- 333031 INDIA
>
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-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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