From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 17:01:01 CDT
Then your psf was somehow improperly generated. I don't know what
went wrong with autopsf, but as a quick fix, checking the option
"regenerate angles dihedrals" in the autopsf menu first may help.
Maybe someone more experienced with autopsf can comment?
On May 29, 2009, at 3:49 PM, firstname.lastname@example.org wrote:
> In the .psf file (there are no angle dihedrals at all; neither for
> nor protein/lipid here):
> 57221 WT1 2 TIP3 OH2 OT -0.834000 15.9994 0
> 57222 WT1 2 TIP3 H1 HT 0.417000 1.0079 0
> 57223 WT1 2 TIP3 H2 HT 0.417000 1.0079 0
> 57224 WT1 3 TIP3 OH2 OT -0.834000 15.9994 0
> 57225 WT1 3 TIP3 H1 HT 0.417000 1.0079 0
> 57226 WT1 3 TIP3 H2 HT 0.417000 1.0079 0
> and in the parameter file (par_all27_prot_lipid.inp) I used I there
> HT OT HT 55.000 104.5200 ! ALLOW WAT
> ! TIP3P GEOMETRY, ADM JR.
> Thanks for your time
>> I have never used autopsf so I can't say for sure what is happening.
>> Can you look at the first few lines of your psf file and confirm that
>> for the water segments, you see auto angles dihedrals?
>> Also, you can check the psf file to check if there are angles present
>> for any water indices.
>> On May 29, 2009, at 2:30 PM, email@example.com wrote:
>>> The modified topology file (using the GUI Autopsf-generator) is the
>>> one as top_all27_prot_lipid.inp only with the bond between the H
>>> Other than that its the same, i.e,
>>> RESI TIP3 0.000 ! tip3p water model, generate using noangle
>>> ATOM OH2 OT -0.834
>>> ATOM H1 HT 0.417
>>> ATOM H2 HT 0.417
>>> BOND OH2 H1 OH2 H2 ! (last bond needed for shake deleted)
>>> ANGLE H1 OH2 H2 ! required
>>> ACCEPTOR OH2
>>> PATCHING FIRS NONE LAST NONE
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