[gmx-users] Parameter preparation of non-standard amino acid

[Mijiddorj B]

Dear GMX users,

I would like to simulate short peptide aggregation. The peptide contains
pyrene moieties instead of phenyl group of phenylalanine. How can I prepare
the parameter for the residue?

Can I also use CgenFF for the short peptide?

Best regards,
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Re: [gmx-users] How to handle calcium ions with charmm36 force field

[sunyeping]

Hello Justin,

Thank you very much!

Best wishes!
Yeping
--
From:Justin Lemkul 
Sent At:2019 Oct. 1 (Tue.) 00:55
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to handle calcium ions with charmm36 force field



On 9/30/19 12:43 PM, sunyeping wrote:
> Dear everyall,
>
> I am trying to do simulations with a protein cotaining calcium ions. When I 
> preprocess the pdb file for the structure with:
>  gmx pdb2gmx -f protein_ca_ligW_0.pdb -o protein.gro
>
> I get the following error:
> Fatal error:
> Atom CA in residue CA 515 was not found in rtp entry CA with 68 atoms
> while sorting atoms.
>
> I checked the  atomtypes.atp file in the charmm36 force field directory and 
> found that the calcium ion seems to be name CAD instead of CA, so I change 
> the calcium atom name from "CA" to "CAD" and run the pdb2gmx command again.  
> This time I got the similar error:
> Fatal error:
> Atom CAD in residue CA 515 was not found in rtp entry CA with 68 atoms
> while sorting atoms.
>
> Now I don't know how to deal with this problems. Could anyone help me?
> Thanks in advance.

What you want is CAL, not CAD, for both the residue and atom name. From 
atomtypes.atp:

CAD112.41100 ; cadmium (II) cation
CAI 12.01100 ; aromatic C next to CPT in trp
CAL 40.08000 ; Calcium Ion

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==
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Re: [gmx-users] How to handle calcium ions with charmm36 force field

[Justin Lemkul]

On 9/30/19 12:43 PM, sunyeping wrote:

Dear everyall,

I am trying to do simulations with a protein cotaining calcium ions. When I 
preprocess the pdb file for the structure with:
 gmx pdb2gmx -f protein_ca_ligW_0.pdb -o protein.gro

I get the following error:
Fatal error:
Atom CA in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

I checked the  atomtypes.atp file in the charmm36 force field directory and found that the calcium 
ion seems to be name CAD instead of CA, so I change the calcium atom name from "CA" to 
"CAD" and run the pdb2gmx command again.  This time I got the similar error:
Fatal error:
Atom CAD in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

Now I don't know how to deal with this problems. Could anyone help me?
Thanks in advance.


What you want is CAL, not CAD, for both the residue and atom name. From 
atomtypes.atp:


   CAD    112.41100 ; cadmium (II) cation
   CAI 12.01100 ; aromatic C next to CPT in trp
   CAL 40.08000 ; Calcium Ion

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] How to handle calcium ions with charmm36 force field

[sunyeping]

Dear everyall,

I am trying to do simulations with a protein cotaining calcium ions. When I 
preprocess the pdb file for the structure with: 
gmx pdb2gmx -f protein_ca_ligW_0.pdb -o protein.gro

I get the following error:
Fatal error:
Atom CA in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

I checked the  atomtypes.atp file in the charmm36 force field directory and 
found that the calcium ion seems to be name CAD instead of CA, so I change the 
calcium atom name from "CA" to "CAD" and run the pdb2gmx command again.  This 
time I got the similar error:
Fatal error:
Atom CAD in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

Now I don't know how to deal with this problems. Could anyone help me? 
Thanks in advance.

Yesping Sun
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[gmx-users] gmx traj ekrot : too many iterations in routine JACOBI

[Marlon Sidore]

Hello,

After the production run (protein in water), I want to get the kinetic
energy through gmx traj. I have a .trr (with velocities, already used
velacc on it) and a .tpr (with the right number of atoms) but I get the
error :
Command: "gmx_mpi traj -f cold_protein.trr -s cold_protein.tpr -ekr
ekrot_wt.xvg -ekt ektrans_wt.xvg"
Error:"
Selected 1: 'Protein'
Reading frame  14 time0.056
Reading frame 120 time0.440
 time0.480
---
Program: gmx traj, version 2018.6
Source file: src/gromacs/linearalgebra/nrjac.cpp (line 165)

Fatal error:
Error: Too many iterations in routine JACOBI
"

This seems strange to me since it happens after 120 frames and not right
away (as I would expect if it was a matter of a mismatch between files). I
can also run the same command, without error, if I omit ekr; ekt only works
fine. The rotational kinetic energy calculation seems to be the problem.

I couldn't find a similar problem in the mailing list. Thanks for your
answers.

Best,

Marlon Sidore

06.69.24.81.94

PhD - Post-doctoral fellow
Institut d’Électronique et des Systèmes (UMR 5214)
860 rue de St Priest
34095 Montpellier cedex 5
FRANCE
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Re: [gmx-users] (no subject)

[Dallas Warren]

Look in, or search the archive, the responses are there.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/

On Mon, 30 Sep. 2019, 1:02 am Mahsa Rezaei, 
wrote:

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
>  them.
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
>
> I made my protein-membrane system with charmm-gui.
>
> so my force is charmm36.
>
> I used the equilibration input files that charmm-gui provide ,
>
> and run 400 ns simulation for equilibration of my system .
>
> RMSD , temperature and pressure is good , so I think my system is stable .
>
> Every thing is good until I use following pull code in my mdp file .
>
> The bilayer does not move and the ligand passes through the membrane
>
> But over time , the length of the z axis increases , and
>
> 4 water molecules are also separated from the membrane.
>
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> 09/29/19,
> 06:30:36 PM
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Re: [gmx-users] various issues when simulating cholesterol membrane

[Justin Lemkul]

On 9/29/19 11:21 PM, Ayesha Fatima wrote:

Dear All,
It has been a futile effort so far when I want to just simulate a simple
cholesterol membrane. I checked the mailing list. but some how my issues
was not really answered.
So after following a few answers and solutions here and there, i would like
to as a few questions  which i cannot solve even after following the
solutions posted.
1. My cholesterol membrane was prepared usingthe CHARMM Membrane BUilder,
hence it sed the xharmm forcefield. There is only 1 charmm forcefield in
Gromacs 2019 Charmm27. so, I downloaded the forcefield and parameter files


Don't use CHARMM27; it's an outdated force field. CHARMM-GUI should give 
you all the necessary GROMACS inputs (topology, .mdp, etc) as well as 
the CHARMM36 force field. Use CHARMM36.


-Justin


Slipids_2016 from the http://www.fos.su.se/~sasha/SLipids/. I used the non
bonded and bonded forcefield parameters given as there is a unique hydrogen
named H3' which is not found in other forcefields such as Gromos53A6 or
54A7.
Although when I used 54A7 parameterised cholesterol.itp from ATB server, i
got the error or naming mismatch which i thinks is because the number of
cholesterol atoms in the ATB file is only 31 while my pdb file has 74 atoms
per molecule and also the atom types are different.
If I use the normal charmm27 forcefield extended to BERGER lipids, error of
proper dihedrals, U-B atoms and i j parameters comes when it reads the
cholesterol.itp.
So when i will want to parametrise the protein, i will have issues or can i
use the same forcefield since the file does have the amino acid parameters
also?
Kindly suggest  what can be the correct way?
Thank you
Regards
Ayesha Fatima


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Position Restraints MD

[Justin Lemkul]

On 9/28/19 2:10 AM, ISHRAT JAHAN wrote:

Thank you sir for the valuable suggestions. I have done distance restraints
on metal and some atoms of amino acids residue as follows-
first generated the distance restrained .itp file using the command
gmx genrestr -f file.gro -n asp83_OD1_Zn.ndx -o distance_restrain.itp
-disre_dist 0.221 -disre_frac 0.221 -disre_up2 0.221 -fc 1000 1000 1000
where 0.221 is the bond length between the OD1 and Zn, and similarly
generated itp files for other atoms also and then added thes files in the
.top file by changing the residue no. accordingly.
perform full md but after the simulation run when i calculated the pairwise
distance between these atoms it shows large fluctuations nearly 0.4 nm.
Please tell whether position restraints have been applied on required atom
or not. If this is not the correct procedure kindly tell the correct
procedure.


I don't think there's any real need to run genrestr; just create the 
topology directive yourself. You can't set every value to the same thing 
(0.221), though. Distance restraints are active over a range - see the 
manual.


If you need help troubleshooting, you will need to provide the actual 
[distance_restraints] contents.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Running iteration for lipid shrinking using InflateGRO methodology

[Justin Lemkul]

On 9/27/19 12:53 PM, Yogesh Sharma wrote:

hello users,

I am using inflategro methodology  to pack lipids around membrane protein.
I used bash script for iteration cycle provided by Justin Lemkul
*. *
But unexpectedly, cycle is dying here
























*gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro
-pbc molWill write gro: Coordinate file in Gromos-87 formatReading file
system_inflated_em.tpr, VERSION 5.1.2 (single precision)Reading file
system_inflated_em.tpr, VERSION 5.1.2 (single precision)Select group for
outputGroup 0 ( System) has  9330 elementsGroup 1 (
  Protein) has  2882 elements.Group12 (
  Other) has  6448 elementsGroup13 (   POPC) has  6448
elementsSelect a group: Selected 0: 'System'Reading frames from gro file
'POPC', 9330 atoms.Reading frame   0 time0.000   Precision of
system_inflated_em.gro is 0.001 (nm)Using output precision of 0.001
(nm)Last frame  0 time0.000
## RUNNING SHRINKING ITERATION
{1..26}...#run_inflategro.sh: 32:
run_inflategro.sh: Illegal number: {1..26}*


Perhaps your version of Bash doesn't like the way I've done the 
iterating. You can use a seq command instead.


-Justin


I used given ( justin lemkul

minim_inflategro.mdp)

with nstlist modified to 10.
  where is it going wrong.
Previous commands:

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top
-r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o
tmp.gro -pbc mol
mv tmp.gro system_inflated_em.gro

perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0
system_shrink1.gro 5 area_shrink1.dat

sh run_inflategro.sh


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Pull Code

[Johannes Hermann]

Dear all,

I have two coordinate files of a system (for state A coord_A.gro and 
state B coord_B.gro). I want to generate configurations (coordinates) 
between these states A and B. How can I apply the pull code to generate 
these configurations? Should I calculate a COM direction first? Can I 
apply -r and -rb as reference position restrains in this case?


Thank you very much in advance!

All the best

Johannes

--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
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Re: [gmx-users] Umbrella sampling on lipid bilayer

[John Whittaker]

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
> them.

Hi,

Justin replied in this mail:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html

Best,

John

>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
>
> I made my protein-membrane system with charmm-gui.
>
> so my force is charmm36.
>
> I used the equilibration input files that charmm-gui provide ,
>
> and run 400 ns simulation for equilibration of my system .
>
> RMSD , temperature and pressure is good , so I think my system is stable .
>
> Every thing is good until I use following pull code in my mdp file .
>
> The bilayer does not move and the ligand passes through the membrane
>
> But over time , the length of the z axis increases , and
>
> 4 water molecules are also separated from the membrane.
>
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
> [image: Mailtrack]
> 
> Sender
> notified by
> Mailtrack
> 
> 09/29/19,
> 06:33:51 PM
> --
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Re: [gmx-users] Gromacs2019 + Gaussian09 QMMM

[Groenhof, Gerrit]

Dear Dmitrii,

Unfortunately, the group nb-search scheme that was needed for QM/MM is 
discontinued. Because it still worked in the 2018 version, I suggest that you 
use the previous version until the problem is fixed.

Use
-DGMX_QMMM_PROGRAM=gaussian
in the cmake command to compile with support. Details on how to link gaussian09 
can be found here:
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
It probably is easiest to use the gau script to make the two programs talk to 
each other.

Good luck,

Gerrit






Dear all,

I am planning to run QM/MM dynamics (ONIOM), following the approach
described here
http://manual.gromacs.org/2019/reference-manual/special/qmmm.html#output

(not the MiMiC, because it has only an additive scheme), Gaussian09 as the
QM package.

However, I could not find any information on compilation of gromacs 2019
with Gaussian, only CP2K for MiMiC support:

http://manual.gromacs.org/documentation/2019/install-guide/index.html

Where I can find the information on the Gromacs2019+Gaussian09 QMMM
installation?

Best,
Dmitrii



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