Hi Eric,
I had a quick look at your attached files.
For me, the problem with your .psf file is the xplor "atom reference numbers" (or what they are correctly called) for TIP3P:
>From your .psf file:
73 WC 8013 TIP3 OH2 75 -0.834000 15.9994 0
74 WC 8013 TIP3 H1 4 0.417000 1.0080 0
75 WC 8013 TIP3 H2 4 0.417000 1.0080 0
>From a new version of the .psf file:
73 W 8013 TIP3 OH2 3 -0.834000 15.9994 0
74 W 8013 TIP3 H1 1 0.417000 1.0080 0
75 W 8013 TIP3 H2 1 0.417000 1.0080 0
Notice 75,4,4 vs. 3,1,1.
Do you use the same topology file for TIP3P for when you use psfgen to get the .psf files as when you run chamber?
I have made new pdf files (both charmm and xplor type) and have run them successful through chamber in ParmEd.
As for the -verbose/no verbose and cmap/nocmap problems I do not know.
Hope you find a solution.
Kind regards,
Sarah
Den 15/09/2014 kl. 22.59 skrev Eric Lang <eric.lang.pg.canterbury.ac.nz>:
> Hello,
>
>
> I would like to run the simulation of a protein in complex with its ligand in a box of TIP3P with the CHARMM 27 force field.
>
>
> I am currently trying to use CHAMBER to convert the PDB/PSF files of my system (generated with PSFGEN in VMD). Although I can generate the correct PRMTOP and INPCRD files for the protein alone, it does not work in the presence of water or with the ligand.
>
>
> I am using a fresh installation of Ambertools 14.12 on Unbuntu 14.04. I used VMD to generate the PSF file but I modified the topology file of the solvate plugin to make sure that it includes the bond between the two hydrogens of TIP3P water. The parameter/topology of the ligand were generated on the Swissparam server.
>
>
> Here is the command entered for the protein alone (which works)
>
>
> chamber -top top_all22_prot_cmap.inp -param par_all22_prot_cmap.inp -xpsf test.psf -crd test.pdb -p test.prmtop -inpcrd test.inpcrd -cmap -verbose
>
>
> It is worth mentionning that without the -verbose flag, it doesn't work: I have a segmentation fault with the following message:
>
> <write_prmtop_header> NPHB 0
>
> Segmentation fault (core dumped) )
>
>
> But it works with the verbose flag.
>
>
> If I do exactly the same for the protein solvated
>
> chamber -top top_all22_prot_cmap.inp -param par_all22_prot_cmap.inp -xpsf test.psf -crd test.pdb -p test.prmtop -inpcrd test.inpcrd -cmap -verbose
>
>
> I got the following:
>
>
> <get_bonded_params> Impropers, TYPES 3384 25
>
> Checking for flag: CMAP
>
> Examining potential match: PSF
>
> Examining potential match: CMAP
>
> CMAP Found
>
> Found 5 unique cmap types:
>
> Type: 1 - 9 11 3 9 11 3 9 11
>
> C NH1 CT1 C NH1 CT1 C NH1
>
> Type: 2 - 9 11 3 9 11 3 9 13
>
> C NH1 CT1 C NH1 CT1 C N
>
> Type: 3 - 9 13 15 9 13 15 9 11
>
> C N CP1 C N CP1 C NH1
>
> Type: 4 - 9 11 5 9 11 5 9 11
>
> C NH1 CT2 C NH1 CT2 C NH1
>
> Type: 5 - 9 11 5 9 11 5 9 13
>
> C NH1 CT2 C NH1 CT2 C N
>
> ============================================================
>
> CMAP parameters assignment index
>
> ============================================================
>
> Dumping entire contents of needed_cmap_types( 5)
>
> needed_cmap_type( 1/ 5)
>
> C NH1 CT1 C NH1 CT1 C NH1 1 1
>
>
>
> However, if I change for -nocmap it works for the solvated protein. But I want to use the CMAP correction for the protein.
>
>
> Does anyone have an idea of what the problem could be?
>
>
>
> Now if I try to include the ligand (and no water) to the protein in CHAMBER
>
>
> chamber -top top_all22_prot_cmap.inp -param par_all22_prot_cmap.inp -str PEP2.par PEP2.rtf -xpsf test.psf -crd test.pdb -p test.prmtop -inpcrd test.inpcrd -verbose -cmap
>
>
> I have the following error:
>
> <get_bonded_params> DIHEDRALS FOUND: 333 out of 276
>
> 920 MISSING dihedral: 255NH1 OR CR C=O
>
> Cannot continue
>
> (same error with -nocmap)
>
>
> I have attached the pdb and psf files of the ligand and some water molecules as well as the .rtf and .par files for the ligand.
>
> If I try to run chamber on this I have the following:
>
>
> chamber -top top_all22_prot_cmap.inp -param par_all22_prot_cmap.inp -str PEP2.par PEP2.rtf -xpsf test.psf -crd test.pdb -p test.prmtop -inpcrd test.inpcrd -verbose -cmap
>
>
> <read_bond_angle_dihe> impropers
>
> <read_bond_angle_dihe> donors
>
> <read_bond_angle_dihe> acceptors
>
> <read_bond_angle_dihe> nonbond
>
> <read_bond_angle_dihe> group
>
> <read_bond_angle_dihe> Done
>
> Checking for flag: CHEQ
>
> Examining potential match: PSF
>
> At line 2774 of file psfprm.F90 (unit = 20, file = 'test.psf')
>
> Fortran runtime error: End of file
>
>
> I have the same error if I specify PSFGEN that I want a CHARMM PSF file (writepsf charmm test.psf)
>
>
> Does anyone has encountered such kind of problem before?
>
> Regarding the ligand, do you think it might come from the way Swissparam write the topology and parameter files?
>
>
> Any help would me much appreciated.
>
>
> Many thanks in advance
>
>
> Eric
>
>
> PS: I tried to use Parmed (downloaded from Jason's GIT) but without success, it cannot read my psf files and for the protein alone I have the following error:
>
> Action chamber failed
>
> ChamberError: Problem assigning parameters to PSF
>
>
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Received on Mon Sep 15 2014 - 16:00:02 PDT
