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but by default, it makes the end groups NH2 & COOH. I want to make it
charged, what modifications are needed?<br><br>
<br><br>
<br>
>>>pdb2gmx will add the end groups for you without any need to
modify .rtp etc... Marc<br><br>
-----Original Message----- From:
<font color="#0000FF"><u>gmx-users-admin@gromacs.org</u></font>
[<a href="mailto:gmx-users-admin@gromacs.org" eudora="autourl">mailto:</a><a href="mailto:gmx-users-admin@gromacs.org" eudora="autourl"><font color="#0000FF"><u>gmx-users-admin@gromacs.org</a></u></font>]On Behalf Of Vivek Raut Sent: Tuesday, August 19, 2003 1:41 PM To: <font color="#0000FF"><u>gmx-users@gromacs.org</u></font> Subject: [gmx-users] how to modify the peptide end groups??<br><br>
hi,<br>
i want to change the end groups of GLY (glycine) segment to NH3+ & COO- . I tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per the atom type defined in ffgmx2.atp. But when i try to make a .gro file for the peptide, it says that its not abel to match the hydrogens from .hdb &. tdb files. is there a more logical way to modify the end groups? if not, then how to modify the .hdb & .tdb files?? <br><br>
<x-sigsep><p></x-sigsep>
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Vivek Raut<br>
Graduate Research Assistant<br>
Department of Bioengineering<br>
Clemson University <br>
Clemson, SC- 29631. USA<br>
Email: vraut@clemson.edu<br>
Phone: 864-650-1431<br>
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