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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