Fwd: [gmx-users] D-form amino acids

[Regina R. Monaco, Ph.D.]

Hi Daan-

	Well, **I** am not worried, but GROMACS won't accept the calculation.  
I am assuming the reason is that the program is not certain what the  
atom types are, what charges to use, and how to index the molecule. At  
least, thats what the error messages indicate  :>

--Regina

On Thursday, May 29, 2003, at 12:08 AM, Daan van Aalten wrote:

>
> Hi
>
> Why worry? As long as you have submitted your entire hexapeptide as one
> molecule and the topology is right it does not matter that your
> molecule is called UNK ?
>
> Daan
>
> On Wed, 28 May 2003, Regina R. Monaco, Ph.D. wrote:
>
>> HI All-
>>
>> 	I am trying to submit a calculation to GROMACS on a hexapeptide
>> composed of D-form amino acids. My input structure file is in the   
>> .mol
>> file format, which I cannot get any program to recognize as being
>> composed of anything other than "UNK" residues. I have tried the
>> (awesome) PRODRG2 (davapc1.bioch.dundee.ac.uk/prodrg/) site, but the
>> .TOP and .ITP output files it generates still have all the residues
>> labelled as "UNK".
>>
>> 	Does anyone know how I can handle this and run an MD simulation?
>>
>> Thanks,
>> Regina Monaco
>>
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>
>
> ####################################################################### 
> #######
>
> Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
> School of Life Sciences                E-mail:  
> dava at davapc1.bioch.dundee.ac.uk
> Univ. of Dundee, Dundee DD1 5EH, UK    WWW:  
> http://davapc1.bioch.dundee.ac.uk
>
>         O     C           O     C         Visit the PRODRG server to  
> take
>         "     |           "     |         the stress out of your  
> topologies!
>   N--c--C--N--C--C--N--C--C--N--C--C--O
>      |           "     |           "       
> http://davapc1.bioch.dundee.ac.uk/
>      C-C-O       O   C-C-C         O              
> programs/prodrg/prodrg.html
>        "
>        O
>
>