True. I guess gromacs groups together the terminal hydrogens, overriding the original force field parameters. Can't say why that decision was made, but it will influence your simulation very little.

Erik

leila karami skrev:
Dear Erik
you said Amber03 was not parameterized with charge groups and last column in your rtp entry holds the chargegroup numbers. but cgnr column in my top file does not looks just like it. in case of H1, H2 and H3. / H1 amber99_17 0.16420 2
//     H2    amber99_17   0.16420     3
//     H3    amber99_17   0.16420     4
//    // /. that's ok. but why
/and my top file is as follow : // // // nr type resnr residue atom cgnr charge mass // //2 amber99_17 1 NGLY H1 2 0.1642 1.008 // 3 amber99_17 1 NGLY H2 2 0.1642 1.008 // 4 amber99_17 1 NGLY H3 2 0.1642 1.008 // / thanks for your attention


--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
er...@xray.bmc.uu.se    http://folding.bmc.uu.se/

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