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Setup, I/O, and Basic questions Jump to new posts
Prepare non-heme irons, 2Fe(III)-2S input files dengwenhao 08/14/20 03:24 AM
Hello all,I'm working with a protein having a non-heme diiron 2FE-2S center.I need to distinguish the two irons to represent the data separately.
So I added iron 1 and iron 2 parameters in the MASS of the .rtf file.
But when running the charmm program to output psf and crd files, the following error is reported in the log file:
WARNING FROM DECODF - COULD NOT CONVERT STRING
FE1
ZERO WILL BE RETURNED.
WARNING FROM DECODF - COULD NOT CONVERT STRING
FE2
ZERO WILL BE RETURNED.
PARRDR> NOTE: atom type "FE1 " is removed from previous group
PARRDR> NOTE: atom type "FE2 " is removed from previous group

PARRDR> ALL ANGLES HAVE POSITIVE MINIMA
Is my way of dealing with the 2 iron 2 sulfur system wrong, or is it a problem of preparation parameters?
Thank you very much for your reply, I added the main part of the input rtf file and the log file to the attachment magager.
PS:I have tried three solutions,None resolved:
1.Use dos2unix command to convert to linux file
2.Use tr -d'\n' new-file.rtf command line,new-file, rtf file is emptied;
3.Using the same FE-O atom type will show duplicate parameters.
0 9 Read More
CHARMM-GUI Jump to new posts
Carry out a simulation using Insulin and a Silica surface. Amo1997 08/13/20 04:35 PM
Hi guys,

I would like to carry out a simulation of insulin on a silica surface. I have devised the following procedure to carry out the necessary simulation but would like to know if I am missing out anything.

Firstly, use the CHARMM gui pdb reader so that I can select the correct insulin monomer (as it allows you to select just chains A and B from a dimer or hexamer model) and have it in the correct protonation state.

Secondly, use the CHARMM gui nanomaterial builder to make a silica that is of the right size and protonation state. VMD to position protein correctly, save as pdb.

Thirdly, use the Multi Component Assembler to combine the two files generated from steps 1 and 2.

From here on use the files generated to carry out a simulation on Ubuntu.

Is this the correct procedure to carry out a viable simulation?

I would like to orientate my protein onto the surface of the silica. Does the Multi - Component Assembler do this or can I just merge the two PDB files from VMD and then carry out a simulation on Ubuntu?

I am relatively new to this and any advice would be much appreciated and go a long way to helping me understand.
0 4 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: water molecules on gromacs simulation to charmm crd format rmv 08/13/20 04:28 PM
CHARMM can read PDB files and write out COOR CARD files.
1 9 Read More
Parameter Set Discussion Jump to new posts
Re: toppar files for GTP-gamma S AnnaBkmn 08/12/20 01:38 PM
Thank you very much for your help!
The column indicating the residue number was not aligned. Everything works now.

Anna.
10 128 Read More
QM/MM Discussion and Questions Jump to new posts
Re: SCCDFTB not converged in qm/mm minimization step Corey Taylor 08/12/20 08:59 AM
If you're sure of your geometry, maybe apply the classic hardware maintenance logic; unplug everything except the bare minimum. So try it with only a couple of QM atoms and see if you can get it to converge then add more to isolate the problem.
4 134 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Write forces in single file lennart 08/12/20 08:34 AM
1. WRITE COOR cannot append to an existing file. You can use the CHARMM SYSTEM command to concatenate this file to an existing file, something like SYSTTEM "cat single_focec.dat >> all_forces.dat"
2. Use COOR FORCE COMP. TEST FIRST is a command for testing (and does more than just compute the force, so is slow).
3. The ENERGY command should do an update, which is necessary.
1 21 Read More
QM/MM Discussion and Questions Jump to new posts
Re: ENDselection terminator missing rmv 08/05/20 03:21 PM
Try breaking the selection into shorter pieces; there are several ways.
  • use the dash char (-) to split into several lines
  • use several defines with shorter selections, combine them in another define or the final command that needs them
  • learn to use selection wildcards such as HC+ and HC1+
1 27 Read More
QM/MM Discussion and Questions Jump to new posts
Re: No parameter for QM-link atom vht 08/05/20 06:23 AM
Thanks you very much.I appreciate your help on this.
3 51 Read More
CHARMM-GUI Jump to new posts
RTFRDR,PARRDR and FCNVRT warnings from topology files cm14sjm 08/03/20 02:48 PM
Hello


I've been trying to do some production runs using files downloaded from the solution builder available in charmmgui for a protein in explicit solvent. I've run the minimisation script, which although runs to completion is full of warnings (attached is the minimisation output file).

I have since tried to so some production runs (the output of these is also attached), but these fail with numerous RTFRDR warnings

***** LEVEL 1 WARNING FROM *****
***** Residue already exists


as well as some from PARRDR

PARRDR> WARNING: ATOMS IN BOND CBD CP 222.50000 1.52700 DONT EXIST
PARRDR> Error: Repeated BOND parameter ( 522): CG2O CG2R is replaced
.....

warnings.

Before a final FCNVRT warning

***** LEVEL 0 WARNING FROM *****
***** Error in conversion: 68NT
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



I think the errors maybe coming from the topology files, but I have not edited the ones I downloaded from charmmgui so I'm unsure how to fix the problem?

Thank you
0 35 Read More
Parameter Set Discussion Jump to new posts
Re: CHARMM parameters for Mn2+ Corey Taylor 08/01/20 08:45 AM
In the interests of transparency and for someone else reading this, my PRES looked like this:

Code
*Additional PRESs for Tf
*
36  1

[...]

PRES TYD         -1.00 !
GROUP
ATOM CZ   CA     -0.18 !
ATOM OH   OH1    -0.82 !
!ATOM HH   H      0.00 !
DELETE ATOM HH

[...]

And corresponding PATCHs in the input file:

Code
*QM/MM calculation of protein, water box
*

BOMBLEV -1

! Read topology and parameter files
stream toppar.str
!##################################
!    COORDINATES
!#################################

!    Read in protein

open read card unit 10 name "prep/6ctc_bp1_prep_prot.pdb"
read sequence pdb resi unit 10
generate Tf setup warn first nter last cter

! Termini, disulfide bonds
patch NTER Tf 1 setup warn
patch CTER Tf 330 setup warn
patch disu Tf 7 Tf 46 setup warn
patch disu Tf 17 Tf 37 setup warn

[...]

open read card unit 10 name "prep/6ctc_bp1_prep_prot.pdb"
read coor pdb resi unit 10

!     Read in metal and counter ions

open read card unit 10 name "prep/6ctc_bp1_prep_FeCO3.pdb"
read sequence pdb unit 10
generate Tf2 setup warn

! Patch Fe-TYR bond
patch TYD  Tf 186 Tf2 331 setup warn

open read card unit 10 name "prep/6ctc_bp1_prep_FeCO3.pdb"
read coor pdb unit 10

[...]
7 851 Read More
Meetings & Events Jump to new posts
LCB Weekly Seminar 2020-2021 Ruben 07/27/20 05:26 PM
Laboratory of Computational Biology weekly seminar series

Meeting announcements for the weekly seminars hosted by the groups of Richard Pastor and Bernard Brooks (Laboratory of Computational Biology, NHLBI, NIH).


Laboratory of Computational Biology
National Heart, Lung and Blood Institute
12 South Drive, Bldg. 12A, Suite 3053
Bethesda, MD 20892-5690


Unless otherwise specified, seminars are currently at Thursday 1:00PM by Zoom

-----------------------------------------------------------------------------------------------------

Date: Aug. 20, 2020
Speaker: Ada Chen
Affiliation: LCB, NHLBI, NIH
Presentation: "Conductance of Ion Channels"

Date: Aug. 27, 2020
Speaker: Mahdi Ghorbani
Affiliation: LCB, NHLBI, NIH
Presentation: TBA

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0 80 Read More
Parameter Set Discussion Jump to new posts
Angle parameter for CG321 CG301 CG321 bond thapa 07/27/20 02:43 PM
Dear charmm users,
Can anyone please help me with good angle parameter for angle C11-C12-C15 (CG321 C301 CG321) of my doxorubicin molecule attached?

I have obtained the following approximate matches.
Approximate matches:
CG2DC2 CG301 CG321 32.00 112.20 ! RETINOL MECH
CG2DC2 CG301 CG331 32.00 112.20 ! RETINOL MECH
CG2O3 CG301 CG331 52.00 108.00 ! AMOL, alpha-methoxy-lactic acid, og
CG2O3 CG301 OG301 45.00 109.00 ! AMOL, alpha-methoxy-lactic acid, og
CG2O3 CG301 OG311 75.70 110.10 ! AMOL, alpha-methoxy-lactic acid, og
CG311 CG301 CG311 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, chayan, 03/06
CG311 CG301 CG321 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, chayan, 03/06
CG311 CG301 CG331 58.35 113.50 11.16 2.561 ! CA, CHOLIC ACID, chayan, 03/06
CG321 CG301 CG331 58.35 113.50 11.16 2.561 ! RETINOL TMCH/MECH
CG331 CG301 CG331 58.35 113.50 11.16 2.561 ! RETINOL TMCH/MECH
CG331 CG301 OG301 45.00 111.50 ! AMOL, alpha-methoxy-lactic acid, og
CG331 CG301 OG302 75.70 110.10 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, chayan
CG331 CG301 OG311 75.70 110.10 ! AMOL, alpha-methoxy-lactic acid, og
CG331 CG301 CLGA3 97.00 111.20 ! TCLE
CG331 CG301 BRGA3 98.00 111.20 ! TBRE
OG301 CG301 OG311 45.00 116.50 ! AMOL, alpha-methoxy-lactic acid, og
CLGA3 CG301 CLGA3 95.00 109.00 ! TCLE
BRGA3 CG301 BRGA3 90.00 110.50 ! TBRE

Thanking you
0 35 Read More
CHARMM-GUI Jump to new posts
Reporting CHARMM-GUI problems rmv 07/23/20 04:52 PM
If you are having difficulty using the CHARMM-GUI web site or the scripts provided there, for the fastest response please use their
contact page.
0 48 Read More
Parameter Set Discussion Jump to new posts
Re: PS lipid headgroup carboxylate improper varies alex 07/23/20 04:37 PM
Yes, it looks like that improper was omitted when the files were created. I've updated toppar_c36_jul20.tgz with the correction. Thanks, alex
1 105 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Couldn't find installation package at obataining CHARMM Flax 07/20/20 06:24 PM
Thanks for your help! It works now.
4 189 Read More
Setup, I/O, and Basic questions Jump to new posts
Error when using restart file cm14sjm 07/20/20 03:40 PM
Hi

I've been trying to do some AXD runs, which require stopping and restarting to get around the time allowance on HPCs.

I've attached the starting input file (1tit_03_001_inp.txt), and the input file to restart the simulation (1tit_03_002_inp.txt). The second input works until the dynamics section when I get the following error:






CHARMM> DYNA CPT leap restart time 0.002 nstep @nstep -
CHARMM> nprint 1000 iprfrq 1000 ISVFRQ 10 ntrfrq 1000 -
CHARMM> iunread 11 iunwri 12 iuncrd 13 iunvel -1 kunit -1 -
CHARMM> nsavc 50000 nsavv 0 -
CHARMM> PCONSTANT pref 1.0 pmass @Pmass pgamma 20.0 -
CHARMM> HOOVER reft @temp tmass 2000.0 tbath @temp firstt @temp
Parameter: NSTEP -> "500000"
Parameter: PMASS -> "3583"
Parameter: TEMP -> "298"
Parameter: TEMP -> "298"
Parameter: TEMP -> "298"
IUNREA = 11 IUNWRI = 12 IUNOS = -1
IUNCRD = 13 IUNVEL = -1 KUNIT = -1
TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON JUN, 10. 2020. JOB
TITLE> * INPUT FILE FOR NPT DYNAMICS OF SOLVATED GLOBULAR PROTEIN
TITLE> * DATE: 7/20/20 15:36:18 CREATED BY USER: cm14sjm
TITLE> *

***** LEVEL 0 WARNING FROM *****
***** Crystal types do not match
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5








I've also tried including the following line from the starting input file:




!
! Image Setup
!

open read unit 10 card name ../../../crystal_image.str
CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma
CRYSTAL READ UNIT 10 CARD

!Image centering by residue
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid @posid .or. segid @negid ) end

!
! Nonbonded Options
!

nbonds atom vatom vfswitch bycb -
ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6
energy

!
!use a restraint to place center of mass of the molecules near the origin
!

MMFP
GEO rcm sphere -
Xref @xcen Yref @ycen Zref @zcen XDIR 1.0 YDIR 1.0 ZDIR 1.0 -
harmonic FORCE 1.0 select .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) end
END





But this gives me this error instead:







CHARMM> nbonds atom vatom vfswitch bycb -
CHARMM> ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
CHARMM> inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
CHARMM> ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6
Parameter: FFTX -> "80"
Parameter: FFTY -> "80"
Parameter: FFTZ -> "80"

***** LEVEL -1 WARNING FROM *****
***** SOME ATOM COORDINATES UNDEFINED OR OUT OF RANGE
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


Does anybody know what I'm doing wrong?

Thank you
0 57 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Error while reading CHARMM36 parameter file hawo 07/19/20 01:24 PM
I see. Yes, it works now. Thanks.
6 183 Read More
General Chemistry Discussions Jump to new posts
how long for explicit protein solution system to relax cm14sjm 07/16/20 04:55 PM
Hello


I am trying do run some protein unfolding simulations in explicit solvent that use the AXD CHARMM module, with input generated using default settings for the protein solution system on the solution builder of charmm gui.

For my code to run I need to give set a value to the parameter events - the number of collisions with a boundary before the trajectory can diffuse across the boundary separating its current box from the next. Events has to be large enough that the system spends enough time in a box for the water to relax around it, and then gets good sampling of the box after water relaxation.

Does anyone have any idea how long it takes for a protein solution system to relax so that I can get an idea of the minimum time I need to confine my protein to each box?

I'm new to charmm and have never used explicit solvents before

Thank you in advance

When doing advanced sampling of protein conformations, how long should it stay in each conformation for the water to relax
0 64 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: selection of 2 atoms error:SELRPN 1 atoms have been selected rmv 07/15/20 03:43 PM
You should see an error message in the output; the square brackets are not part of the syntax

The documentation suggests a single atom selection is used, with an .OR. operator
1 76 Read More
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