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how to write Protein ligand complex psf file
#37497 05/14/19 03:13 PM
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nawel Offline OP
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Dear Charmm user,

I am trying to perform an MD simulation of a protein and ligand complex. I created the topology and parameter file for my ligand thanks to CGenFF webpage. From that I was able to generate the PSF files for my protein and ligand separately but once I want to combine the two I am confused on the way to do that.
My attempt is to generate a psf file for the combine system using this input file (attached file) but I am very confused with the use of append and flex when uploading the PARA and RTF files.

Can someone guide me on the procedure for a ligand-protein simulation with charmm?

Many thanks in advance,

Best regards,

Nawel

Attached Files
generate_psf.txt (1.37 KB, 91 downloads)
Re: how to write Protein ligand complex psf file
nawel #37498 05/14/19 03:53 PM
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All but the first RTF/PARAM file pair must include the APPEND option (which you have done).

If FLEX is used, all PARAM files must be read with the FLEX keyword (which you have not done).


Rick Venable
computational chemist

Re: how to write Protein ligand complex psf file
rmv #37500 05/15/19 09:03 AM
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nawel Offline OP
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Many thanks for your quick reply,

When I add FLEX for all the PARA files I obtained these warnings for the protein_ligand para file:

"""
CHARMM>

CHARMM> ! Read RTF
CHARMM> open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all36_prot_lipid.rtf"
VOPEN> Attempting to open::/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all36_prot_lipid.rtf::
OPNLGU> Unit 1 opened for READONLY access to /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/top_all36_prot_lipid.rtf

CHARMM> read rtf card unit 1
MAINIO> Residue topology file being read from unit 1.
TITLE> *> CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS AND LIPIDS <<
TITLE> *>>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> JULY 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM>

CHARMM> ! Read PARA
CHARMM> open unit 1 card read name "/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all36_prot_lipid.prm"
VOPEN> Attempting to open::/sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all36_prot_lipid.prm::
OPNLGU> Unit 1 opened for READONLY access to /sge/packs/packs_centos/opt/CHARMM_CentOS6/c36b1/toppar/par_all36_prot_lipid.prm

CHARMM> read para card unit 1 flex

PARAMETER FILE BEING READ FROM UNIT 1
TITLE> *>CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS AND LIPIDS <<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> JULY, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARRDR> WARNING: ATOMS IN BOND NH2 CT1 240.00000 1.45500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CST OST 937.96000 1.16000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND SS FE 250.00000 2.32000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND C C 600.00000 1.33500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CA CA 305.00000 1.37500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CE1 CE1 440.00000 1.34000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CE1 CE2 500.00000 1.34200 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CE1 CT2 365.00000 1.50200 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CE1 CT3 383.00000 1.50400 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CE2 CE2 510.00000 1.33000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CP1 C 250.00000 1.49000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CP1 CC 250.00000 1.49000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CP1 CD 200.00000 1.49000 DONT EXIST

........

which conducts to this error:

CHARMM> ! Read PDB seq
CHARMM> open unit 1 card read name "2q5a_mono_charmm_noh.pdb"
VOPEN> Attempting to open::2q5a_mono_charmm_noh.pdb::
OPNLGU> Unit 1 opened for READONLY access to 2q5a_mono_charmm_noh.pdb

CHARMM> read sequ pdb unit 1
MAINIO> Sequence information being read from unit 1.
TITLE> *

RESIDUE SEQUENCE -- 157 RESIDUES
LEU PRO PRO GLY TRP GLU LYS ALA MET SER ARG SER SER GLY ARG VAL TYR TYR PHE ASN
HSE ILE THR ASN ALA SER GLN TRP GLU ARG PRO SER GLY GLY ASN SER SER SER GLY LYS
ASN GLY GLN GLY GLU PRO ALA ARG VAL ARG CYS SER HSE LEU LEU VAL LYS HSE SER GLN
SER ARG ARG PRO SER SER TRP ARG GLN GLU LYS ILE THR ARG THR LYS GLU GLU ALA LEU
GLU LEU ILE ASN GLY TYR ILE GLN LYS ILE LYS SER GLY GLU GLU ASP PHE GLU SER LEU
ALA SER GLN PHE SER ASP CYS SER SER ALA LYS ALA ARG GLY ASP LEU GLY ALA PHE SER
ARG GLY GLN MET GLN LYS PRO PHE GLU ASP ALA SER PHE ALA LEU ARG THR GLY GLU MET
SER GLY PRO VAL PHE THR ASP SER GLY ILE HSD ILE ILE LEU ARG THR GLU
***** Message from SEQRDR ***** THE SYSTEM CONTAINS 30 TITRATABLE GROUPS
THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF
HIS - 0 ASP - 5 GLU - 13 LYS - 9 TYR - 3

CHARMM>

CHARMM> generate complex setup ! Command to generate the psf
THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE
: No atom parameters for atom 1 type 56
: No atom parameters for atom 2 type 2
: No atom parameters for atom 5 type 22
: No atom parameters for atom 6 type 6
: No atom parameters for atom 7 type 23
: No atom parameters for atom 8 type 3
: No atom parameters for atom 12 type 24
: No atom parameters for atom 20 type 20
: No atom parameters for atom 21 type 70
: No atom parameters for atom 22 type 50
: No atom parameters for atom 23 type 31

...


I feel like it the protein parameters have not been read properly??


I have attached the output file so you can see better.

Attached Files
comb_psf.txt (246.43 KB, 59 downloads)
Last edited by nawel; 05/15/19 09:04 AM.
Re: how to write Protein ligand complex psf file
nawel #37501 05/15/19 02:41 PM
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It appears you are not using the distributed files; there are no such files as top_all36_prot_lipid.rtf or par_all36_prot_lipid.prm in the C36 distribution. The lipid and protein files are separate, and it appears that someone has combined them in a way that is incorrect.


Rick Venable
computational chemist

Re: how to write Protein ligand complex psf file
rmv #37502 05/16/19 09:51 AM
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nawel Offline OP
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Thanks for noticing that. I downloaded the correct files on the Mackerell webpage but now I get errors straight on the loading of the new rtf file:

Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 36b1 August 15, 2011
Git commit ID 093ce0e
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-573.18.1.el6.x86_64(x86_64)@pip
Created on 5/16/19 at 11:44:51 by user: mele

Maximum number of ATOMS: 360720, and RESidues: 120240
RDTITL> * CREATE PSF
RDTITL> *

CHARMM>

CHARMM> ! Read RTF
CHARMM> open unit 1 card read name "top_all36_prot.rtf"
VOPEN> Attempting to open::top_all36_prot.rtf::
OPNLGU> Unit 1 opened for READONLY access to top_all36_prot.rtf

CHARMM> read rtf card unit 1
MAINIO> Residue topology file being read from unit 1.
TITLE> *>>>>>>>>CHARMM36 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>>> MAY 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 H 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 HC 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 HA 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 HP 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
MASS -1 HB1 1.00800
**** ERROR in RTFRDR **** Bad atom type code = -1 was specified. It was ignored.
......


I am so confused on what to do any more. When I was using the combined file with only the protein I did not had any issue and now whichever file I used I got a problem.

Re: how to write Protein ligand complex psf file
nawel #37503 05/16/19 02:58 PM
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Your CHARMM version is too old to use the new files; c43b2 is available, and there is no fee if you do not plan to use DOMDEC, a fast MD engine employing domain decomposition (registration is required).

The introduction of "MASS -1" for CHARMM version c39 and later is clearly explained on the page linked to by the "CHARMM Force Fields" item under the Resources menu on the main charmm.org site.

There is also a link for downloading the older form of the parameters, which may work with what you have, but an upgrade to a recent CHARMM version is probably a good idea.


Rick Venable
computational chemist

Re: how to write Protein ligand complex psf file
rmv #37507 05/20/19 09:06 AM
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nawel Offline OP
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Sorry for the late reply.

Unfortunately can not upgrade my CHARMM version. So when I use the parameters files individually it is ok but when I used them together (CGenFF and protein) it can't works. So one option would be to use an older version of both force fields parameters??

Many thanks


Moderated by  John Legato, lennart 

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