Hi Fabian,
When leap loads your PDB file, this message:
> Unknown residue: RIT
indicates that it doesn't know what type of residue "RIT" is.
In your lib file, you defined a residue named "RIT1":
> !!index array str
> "RIT1"
If you go back and change that to RIT, things should work better.
On Sun, Mar 30, 2014 at 5:49 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
> Hi Aldo and all,
>
> I tried your suggestion, but I am probably doing something wrong, the creation of the .lib and ..prmtop .inpcrd files for both copies go smoothly, but then when I tried to upload the complex of both molecules or even only one as explained in the antechamber tutorial (http://ambermd.org/tutorials/basic/tutorial4b/) this is the result:
>
> AMBER General Force Field for organic molecules (Version 1.5, January 2013)
>> loadamberparams RIT1.frcmod
> Loading parameters: ./RIT1.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
>> loadoff RIT1.lib
> Loading library: ./RIT1.lib
>> RIT = loadpdb RIT1.pdb
> Loading PDB file: ./RIT1.pdb
> Unknown residue: RIT number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: RIT sequence: 1
> Created a new atom named: C1 within residue: .R<RIT 1>
> Created a new atom named: C2 within residue: .R<RIT 1>
> Created a new atom named: C3 within residue: .R<RIT 1>
> Created a new atom named: C4 within residue: .R<RIT 1>
> Created a new atom named: N1 within residue: .R<RIT 1>
> Created a new atom named: C5 within residue: .R<RIT 1>
> Created a new atom named: C6 within residue: .R<RIT 1>
> Created a new atom named: S1 within residue: .R<RIT 1>
> .....
>
> Weird because the .lib file looks good:
>
> !!index array str
> "RIT1"
> !entry.RIT1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
> "C1" "c3" 0 1 131072 1 6 -0.097100
> "C2" "c3" 0 1 131072 2 6 -0.098000
> "C3" "c3" 0 1 131072 3 6 -0.097100
> "C4" "cc" 0 1 131072 4 6 0.398700
> "N1" "nd" 0 1 131072 5 7 -0.641000
>
>
> and the .pdb file has the same names:
>
> HETATM 1 C1 RIT 1 -10.994 -7.824 6.364 1.00 0.00 C
> HETATM 2 C2 RIT 1 -10.520 -8.901 5.385 1.00 0.00 C
> HETATM 3 C3 RIT 1 -11.033 -10.268 5.843 1.00 0.00 C
> HETATM 4 C4 RIT 1 -11.054 -8.599 4.009 1.00 0.00 C
> HETATM 5 N1 RIT 1 -10.391 -8.378 2.897 1.00 0.00 N
> HETATM 6 C5 RIT 1 -11.014 -8.121 1.766 1.00 0.00 C
> HETATM 7 C6 RIT 1 -12.371 -8.101 1.766 1.00 0.00 C
>
>
> What is the problem?
>
> Thanks a lot,
>
> Fabian
>
>
>
>
> On Mar 27, 2014, at 3:40 PM, Aldo Segura <asegurac666.yahoo.com.mx> wrote:
>
>> Hi Fabian,
>>
>> Are the two molecules the same drug? If this is the case, you just need to get parameters for one molecule. Otherwise, you need to perform the same procedure for each one of the two drugs. For instance, you'll get a set of files for each drug and you should be able to call them inside your leap script.
>>
>> Best,
>>
>> Aldo
>>
>>
>> =======================================
>> Aldo Segura-Cabrera
>> Postdoctoral Fellow
>> Division of Experimental Hematology and Cancer Biology
>> Cancer and Blood Diseases Institute
>> Cincinnati Children's Hospital Medical Center
>> 3333 Burnet Ave, MLC
>> 7013, Cincinnati OH 45229
>>
>> =========================================
>>
>>
>>
>> El Jueves, 27 de marzo, 2014 9:23:14, Fabian Glaser <fglaser.technion.ac.il> escribió:
>>
>> Thanks a lot,
>>
>> OK, could you please suggest a good alternative to parametrize two drug like molecules for MD on amber??
>>
>> Or it is the wrong tool?
>>
>> Thanks a lot,
>>
>> Fabian
>>
>>
>>
>> On Mar 27, 2014, at 3:19 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>>
>>> On Thu, Mar 27, 2014, Fabian Glaser wrote:
>>>>
>>>> I am trying to use antechamber for a drug, which works great for
>>>> one molecule, but if I use a pdb with two copies of the
>> molecule,
>>>> antechamber never ends:
>>>>
>>>> Total number of electrons: 768; net charge: 0
>>>>
>>>> Running: /Users/fabian/TOOLS/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
>>>
>>> This is a very large system; beyond that, sqm is trying to find an energy
>>> minimum. If you have two molecules, the energy minimum might be with the
>>> molecules arbitarily far apart, and sqm will never complete the job.
>>>
>>> Short answer: don't do that. Antechamber is designed to work with single
>>> molecules.
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________
>> Fabian Glaser, PhD
>>
>> Head of the Structural Bioinformatics section
>> Bioinformatics Knowledge Unit - BKU
>>
>> The Lorry I. Lokey Interdisciplinary
>> Center for Life Sciences and Engineering
>> Technion - Israel Institute of Technology
>> Haifa 32000, ISRAEL
>>
>> fglaser.technion.ac.il
>> Tel: +972 4 8293701
>> Fax: +972 4 8225153
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________
> Fabian Glaser, PhD
>
> Head of the Structural Bioinformatics section
> Bioinformatics Knowledge Unit - BKU
>
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
>
> fglaser.technion.ac.il
> Tel: +972 4 8293701
> Fax: +972 4 8225153
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Mar 30 2014 - 07:30:03 PDT
