Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand

From: Sarah Witzke <witzke.sdu.dk>
Date: Tue, 16 Sep 2014 14:20:25 +0000

Hi Erik,

Good that you got a bit further :-) File format conversion is a lot funů or not.

WIthout having your files it's a bit difficult, but from the top of my head:
Have you check if you have this line at the end of your .psf file (before the CMAP terms):
       0 0 !NUMLP NUMLPH
Non-parmed-chamber used to be sensitive to this.

I have not used non-parmed-chamer in the amber package for a long time since I had several issues it could not handle for my particular system, so I am not up to date on any development there.

If you like, you can send me your .psf, .pdb, .rtf, .par and .str files and I can play around a little.

Maybe someone else have an explanation?

Kind regards,
Sarah


Den 16/09/2014 kl. 15.52 skrev Eric Lang <eric.lang.pg.canterbury.ac.nz>:

> 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 - 07:30:02 PDT
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