Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER.
Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan On 26 September 2011 17:35, Yun Shi <yunsh...@gmail.com> wrote: > Hi all, > > I just noted that the tip3p water converted from amber format to gromacs > format is > > [ moleculetype ] > ; molname nrexcl ; TIP3P model > WAT 2 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > 1 OW 1 WAT O 1 -0.834 16.00000 > 2 HW 1 WAT H1 1 0.417 1.00800 > 3 HW 1 WAT H2 1 0.417 1.00800 > > #ifdef FLEXIBLE > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 462750.4 0.09572 462750.4 > 1 3 1 0.09572 462750.4 0.09572 462750.4 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.520 836.800 104.520 836.800 > #else > [ settles ] > ; i j funct length > 1 1 0.09572 0.15139 > > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > #endif > > > while in amber99sb.ff/tip3p.itp. it is > > moleculetype ] > ; molname nrexcl > SOL 2 > > [ atoms ] > ; id at type res nr res name at name cg nr charge mass > 1 OW 1 SOL OW 1 -0.834 16.00000 > 2 HW 1 SOL HW1 1 0.417 1.00800 > 3 HW 1 SOL HW2 1 0.417 1.00800 > > #ifndef FLEXIBLE > > [ settles ] > ; OW funct doh dhh > 1 1 0.09572 0.15139 > > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > > #else > > [ bonds ] > ; i j funct length force_constant > 1 2 1 0.09572 502416.0 0.09572 502416.0 > 1 3 1 0.09572 502416.0 0.09572 502416.0 > > > [ angles ] > ; i j k funct angle force_constant > 2 1 3 1 104.52 628.02 104.52 628.02 > > #endif > > So it seems that the force_constants for O-H bond and H-O-H angle are > different? Does this mean amber and gromacs use different parameters for > tip3p water? or it's just acpype is not working right? > > Thanks, > Yun > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
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