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

From: Eric Lang <eric.lang.pg.canterbury.ac.nz>
Date: Mon, 15 Sep 2014 20:59:53 +0000

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 - 14:30:02 PDT
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