Hi Sarah,
Thanks a lot for your quick reply and for having tried ParmEd with my files. I have been able to generate the Amber files for the ligand+water with ParmEd
Actually the atom reference number wasn't the problem: I had a look and basically I have different numbers because I use a slightly older version of the CHARMM22 toppology file (which includes TIP3P) and the atoms composing the TIP3P are defined at a different position than in your topology file and thus have a different reference number:
In my case:
MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
....
MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN
While in your case you probably used toppar_water_ions.str, in which:
MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN
...
MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN
But since you managed to generate the Amber files with ParmEd I tried this approach and I found my mistake: I specified PEP2.rtf with the flag -str instead of -top. By modifying this, I have been able to generate the prmtop and inpcrd files for the ligand and the water molecules, which is a very encouraging first step.
However, even when using the same atom reference numbers as you have, I cannot generate the files directly in CHAMBER:
Running:
chamber -top top_all22_prot.rtf -param par_all22_prot.prm -str PEP2.par PEP2.rtf toppar_water_ions.str -xpsf test.psf -crd test.pdb -p test.prmtop -inpcrd test.inpcrd -verbose -cmap
give me:
<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
Moreover, using Parmed, I cannot generate the AMBER files for the protein itself.
For example running:
chamber -top top_all22_prot.rtf -param par_all22_prot.prm -str toppar_water_ions.str -psf test.psf -crd test.pdb
where test.pdb and test.psf correspond to my protein alone, I have the following error:
Action chamber failed
ChamberError: Problem assigning parameters to PSF
So to summarize, I can generate the AMBER files for the ligand and water with Parmed, generate those for the protein alone in Chamber, but it doesn't work for my full system.
Any idea of what the problem could be?
Many thanks in advance for your help!
Eric
________________________________
From: "Sarah Witzke" <witzke.sdu.dk<mailto:witzke.sdu.dk>>
Date: Sep 15, 2014 11:47 PM
Subject: Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand
To: "AMBER Mailing List" <amber.ambermd.org<mailto:amber.ambermd.org>>
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<mailto: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 Tue Sep 16 2014 - 07:00:02 PDT
