[gmx-users] Concatenating trajectories

[Pandya, Akash]

Hi,

I have four trajectories of the same condition (protein only) that I want to 
concatenate. I used the command below to do this:

gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc -cat

So this command gives me a file with all four trajectories, pasted together. 
The combined trajectory has now got four sets of the same time stamps. My 
question is how can I change the time stamps so that they appear in 
chronological order, instead of repeated time stamps?. So I would have a 
combined trajectory e.g. 20 to 200 ns.

I hope I'm being clear about what I want to do and someone can guide me on 
achieving this.

Best wishes,

Akash




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[gmx-users] RDF calculation from surface of protein

[Pandya, Akash]

Hi all,

I am trying to calculate the RDF between the protein surface and the centre of 
mass of my ligand and water molecules. Please find below the command I used:

gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 
-cn number.xvg -surf mol -seltype mol_com


I get the following error:



Inconsistency in user input:
-surf only works with -ref that consists of atoms

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am wondering what this error means? My ref group does contain atoms? Any 
guidance will be much appreciated :)


Akash
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[gmx-users] Diffusion Coefficient for hydration waters

[Pandya, Akash]

Hi all,

The diffusion coefficient can be calculated for the all the waters in the 
system, but how do calculate it for just the water molecules which are within 
0.5 nm of the protein? Does anyone have any experience with this?

I've tried to use gmx select to write an index file for the waters but as this 
is a dynamic selection, I would have to calculate each frame individually.

Akash
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[gmx-users] How to calculate the number of ligand and water molecules around protein?

[Pandya, Akash]

Hi all,

I wanted to ask about the best way to calculate the number of ligand molecules 
and water molecules around my protein at certain cut-off. I have used gmx 
trjorder -nshell  and   gmx select -os. Both have given me 
different results, so I wanted to know if anyone has had any luck with either 
to an accurate degree? Any guidance will be much appreciated.

Akash
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[gmx-users] Hydrogen bonding criteria in Gromacs

[Pandya, Akash]

Hi all,

I  wanted to ask a couple of questions about the hydrogen bonding calculation 
in Gromacs.


  1.   Why is the default angle cutoff 30 degrees? The reason I ask this is 
because I’ve seen in other packages with higher angle cutoffs.
  2.  What’s the best way to define cutoffs for my system? I know this is 
ambiguous, but is there a procedure I can use to decide?

Any guidance will be much appreciated.

Thank you,

Akash

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[gmx-users] Question about the SASA value per residue

[Pandya, Akash]

Hi all,

I have a quick question about the value obtained for the SASA calculation on a 
per residue basis (-or flag). Is this value the absolute SASA for each residue?

Best wishes,

Akash
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[gmx-users] SASA calculation in Gromacs

[Pandya, Akash]

Hi all,

I calculated the SASA on a per residue basis using the flag -or and I have 
values ranging from 0 to 1.88 nm2 . My question is how can I determine the 
thresholds between buried/exposed residues? I did a literature search, but was 
unable to find any literature. Any guidance would be much appreciated.


Best wishes,

Akash
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[gmx-users] gmx trjorder

[Pandya, Akash]

Hi,

I would like to calculate the number of ligand molecules within 0.5 nm of a 
particular amino acid in my protein. I came across the gmx trjorder command (as 
shown below).


gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b 
2 -e 4 -na 10 -r 0.5


I have 10 atoms in my ligand. I wanted to ask how accurate is this command in 
trying to calculate what I want?


Akash

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[gmx-users] Hydrogen Bond analysis

[Pandya, Akash]

Hi all,

This may sound like a stupid question, but is there a "selection process" 
within gromacs whereby I can determine the correct donor-acceptor distance and 
angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing 
various literature that study protein-water/ protein-ligand/ligand-water 
interactions, the authors seem to use varying cut-offs e.g. 0.35/0.24 nm. I 
know 0.35 nm is used for moderate hydrogen bond and 0.24 nm is a strong 
hydrogen bond. So basically what I am asking is how do I find the optimum 
cut-off values? Do I simply use trial and error? Or can I used other gromacs 
utilities such as gmx gangle and distance to help me make a decision?

Akash
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[gmx-users] Ligand molecule occupancy

[Pandya, Akash]

Hi,

I have multiple ligand molecules of the same type in my system. If I wanted to 
monitor the Cartesian coordinates of each individual ligand during a 
simulation, is there a Gromacs tool to do that? or do I have write a custom 
script?

Some background:
My purpose is to look at binding/unbinding events for each ligand individually. 
I have calculated the minimum distance between protein residues and ligands in 
my system, but this does not give the identity of the ligand (e.g. resid or 
atom number) within a particular cut-off. I used the gmx pairdist module in 
Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,

Akash
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[gmx-users] gmx trjorder help

[Pandya, Akash]

Hi,


I used gmx trjorder to order my ligand molecules based on the distance from the 
COM of my protein using the command below:

gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -o ordered.gro -nshell 
nshell1.xvg -b 2 -e 2 -na 10 -r 0.5



I viewed the nshell1.xvg file to see how many ligand molecules were found 
within the shell at a particular time. I know in the gromacs manual it says 
"When an index group of the first n waters is made, the ordered trajectory can 
be used with any GROMACS program to analyze the n closest waters". I presume 
that I can use this for my ligand molecules too.

The problem I have with this is the "ordered" trajectory file contains all the 
ligand molecules even the ones not within the cut-off. Can anybody help with 
this?


Akash

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[gmx-users] gmx pairdist help

[Pandya, Akash]

Hi all,

I'm trying calculate the pairwise distance between each of my protein residues 
and my ligand molecules. I type the following command:

gmx pairdist -f Traj.xtc -s Traj.tpr -n mindist.ndx -selrpos whole_res_com 
-refgrouping res -o dist.xvg -type min

When I don't type the "-selrpos whole_res_com" I get the same values so by 
default is it working out from the COM of each individual residue?

Akash



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[gmx-users] Obtaining AMBER parameters for Mn2+ and zwitterion form Arginine

[Pandya, Akash]

Hi,

I have found a AMBER database with the Mn2+ ion and Arginine (zwitterion) from 
the following link:

http://research.bmh.manchester.ac.uk/bryce/amber

How can I convert these parameters so that I can use them in Gromacs. Any help 
would be much appreciated.

Best wishes,

Akash
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[gmx-users] Spatial Distribution Function

[Pandya, Akash]

Hi all,

I'm trying to generate a spatial distribution function for my ligands around my 
protein. I read in the manual I can bypass the gmx trjconv steps if I wanted to 
calculate the SDF for arbitrary Cartesian coordinates. The command I used is 
shown below:

gmx spatial -f protein_LIG.gro -s protein.tpr -n LIG.ndx -b 2 -e 6 -w 
yes -nab 10

I selected the LIG group for the SDF calculation and selected the protein and 
LIG group for the output coordinates. Is this correct? Any help would be much 
appreciated.


Best wishes,

Akash
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[gmx-users] Obtaining AMBER parameter for Zwitterion Amino acids to use in Gromacs

[Pandya, Akash]

Hi,

I have found a AMBER database which contains the parameters for zwitterion 
amino acids from the link below:

http://research.bmh.manchester.ac.uk/bryce/amber/

Does anyone know how to extract the parameters to use in Gromacs?


Akash
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Re: [gmx-users] SASA calculation

[Pandya, Akash]

I already figured out how to get a SASA value for each residue. But I'm asking 
if there is any threshold in place where I can determine whether the residue is 
exposed or buried?

And also is the SASA value for each residue given as the relative SASA in 
gromacs?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Bratin Kumar 
Das
Sent: 22 August 2019 03:45
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] SASA calculation

You can put the residue of your interest inside a .ndx file..Use the .ndx file 
when you are running sasa command

On Wed 21 Aug, 2019, 11:25 PM Pandya, Akash, 
wrote:

> Hi all,
>
> I calculated the SASA for my protein and I got the average area per 
> residue. I was wondering if there was a criteria to determine whether 
> a residue is exposed or buried based on an individual's SASA? Or is it 
> arbitrary? Apologies if I'm being naive, it's just that I've never 
> actually used this calculation before. Thank you for your help.
>
> Best wishes,
>
> Akash
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[gmx-users] SASA calculation

[Pandya, Akash]

Hi all,

I calculated the SASA for my protein and I got the average area per residue. I 
was wondering if there was a criteria to determine whether a residue is exposed 
or buried based on an individual's SASA? Or is it arbitrary? Apologies if I'm 
being naive, it's just that I've never actually used this calculation before. 
Thank you for your help.

Best wishes,

Akash
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Re: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

[Pandya, Akash]

Do I still need to do this if I just want charged arginine (CARG)? Its my 
understanding that there are three types of arginine residues;  ARG, CARG and 
NARG available. I thought the amino acids are available in gromacs? Sorry if 
it's a silly question to ask, but I have not used the Amber FF in gromacs 
before. 

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of ABEL Stephane
Sent: 02 July 2019 16:18
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Help with generating Arginine topology for Amber FF 
(Pandya, Akash)

Hello 

there are not parameters and RESP charges for standalone residue such as Arg in 
GROMACS. So you will have to construct a rtp file for this residue and derive 
the corresponding RESP charges yourself. You could also do a quick in 
literature to see if some have already done the job for you. 

Good luck

Stefane

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[gmx-users] Help with generating Arginine topology for Amber FF

[Pandya, Akash]

Hi all,

I'm trying to generate topology for arginine. I use the following command:

gmx pdb2gmx -f Arginine.pdb -o Arg.gro -inter -water tip3p

I get the following error:

Fatal error:
In the chosen force field there is no residue type for 'ARG' as a standalone
(starting & ending) residue

Please can someone guide me on how to solve this issue?

This is my coordinate file:

ATOM  1  O   ARG A   1   3.163   0.755   1.217  1.00  0.00   O1-
ATOM  2  OXT ARG A   1   3.741   0.815  -0.992  1.00  0.00   O
ATOM  3  NE  ARG A   1  -2.229  -0.118  -0.364  1.00  0.00   N1+
ATOM  4  N   ARG A   1   2.680  -1.912   0.462  1.00  0.00   N
ATOM  5  NH1 ARG A   1  -4.417  -1.176  -0.271  1.00  0.00   N
ATOM  6  NH2 ARG A   1  -4.077   0.991   0.701  1.00  0.00   N
ATOM  7  CB  ARG A   1   0.686  -0.545   0.119  1.00  0.00   C
ATOM  8  CG  ARG A   1   0.099   0.711  -0.538  1.00  0.00   C
ATOM  9  CA  ARG A   1   2.142  -0.780  -0.295  1.00  0.00   C
ATOM 10  CD  ARG A   1  -1.326   0.993  -0.070  1.00  0.00   C
ATOM 11  C   ARG A   1   3.109   0.376   0.014  1.00  0.00   C
ATOM 12  CZ  ARG A   1  -3.572  -0.110   0.017  1.00  0.00   C
ATOM 13  HB1 ARG A   1   0.090  -1.427  -0.144  1.00  0.00   H
ATOM 14  HB2 ARG A   1   0.620  -0.431   1.210  1.00  0.00   H
ATOM 15  HG1 ARG A   1   0.715   1.588  -0.312  1.00  0.00   H
ATOM 16  HG2 ARG A   1   0.104   0.580  -1.627  1.00  0.00   H
ATOM 17  HA  ARG A   1   2.179  -1.018  -1.366  1.00  0.00   H
ATOM 18  HD1 ARG A   1  -1.699   1.886  -0.583  1.00  0.00   H
ATOM 19  HD2 ARG A   1  -1.323   1.163   1.012  1.00  0.00   H
ATOM 20  HE  ARG A   1  -1.895  -0.929  -0.880  1.00  0.00   H
ATOM 21  H1  ARG A   1   3.603  -2.156   0.104  1.00  0.00   H
ATOM 22  H2  ARG A   1   2.095  -2.733   0.313  1.00  0.00   H
ATOM 23 HH11 ARG A   1  -4.078  -1.995  -0.770  1.00  0.00   H
ATOM 24 HH12 ARG A   1  -5.395  -1.165   0.009  1.00  0.00   H
ATOM 25 HH21 ARG A   1  -3.505   1.798   0.934  1.00  0.00   H
ATOM 26 HH22 ARG A   1  -5.052   1.019   0.990  1.00  0.00   H
CONECT1   11
CONECT2   11
CONECT3   10   12   20
CONECT49   21   22
CONECT5   12   23   24
CONECT6   12   25   26
CONECT789   13   14
CONECT87   10   15   16
CONECT947   11   17
CONECT   1038   18   19
CONECT   11129
CONECT   12356
CONECT   137
CONECT   147
CONECT   158
CONECT   168
CONECT   179
CONECT   18   10
CONECT   19   10
CONECT   203
CONECT   214
CONECT   224
CONECT   235
CONECT   245
CONECT   256
CONECT   266
MASTER00000000   260   260
END

Thanks,

Akash

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[gmx-users] Topology for CARG for Amber94 FF

[Pandya, Akash]

Hi all,

I'm trying to generate a topology for CARG using pdb2gmx for Amber94 FF but I'm 
getting this error :

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).

Could someone please guide me on how to fix this error?

Akash
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[gmx-users] Citrate topology in Charmm36 FF

[Pandya, Akash]

Hi all,

I'm simulating Citrate in water using the Charmm36 FF. I get this error in my 
topology. I have used the same topology for charmm27 ff and had no problems.



ERROR 1 [file CITMolecule.itp, line 63]:
  No default Bond types


ERROR 2 [file CITMolecule.itp, line 64]:
  No default Bond types


ERROR 3 [file CITMolecule.itp, line 71]:
  No default Bond types


ERROR 4 [file CITMolecule.itp, line 72]:
  No default Bond types


ERROR 5 [file CITMolecule.itp, line 81]:
  No default U-B types


ERROR 6 [file CITMolecule.itp, line 82]:
  No default U-B types


ERROR 7 [file CITMolecule.itp, line 84]:
  No default U-B types


ERROR 8 [file CITMolecule.itp, line 97]:
  No default U-B types


ERROR 9 [file CITMolecule.itp, line 98]:
  No default U-B types


ERROR 10 [file CITMolecule.itp, line 100]:
  No default U-B types


My topology file is pasted here with the relevant parts:


[ bondtypes ]
CC OC  1  0.126 439320.0
OH1H   1  0.096 456056.0
CT CC  1  0.152 167360.0
CT2CT  1  0.150 186188.0
CT OH1 1  0.142 358150.4

[ angletypes ]
OCCCOC  5 124.00   836.80   0.2225   58576.000
OCCC   CT2  5 118.00   334.72   0.2388   41840.000
CTCCOC  5 118.00   334.72   0.2388   41840.000
CT2   CTCC  5 108.00   435.14   0.   0.000
CT2   CT   CT2  5 113.60   488.27   0.25619338.688
HA   CT2CT  5 110.10   279.74   0.2179   18853.104
CC   CT2CT  5 108.00   435.14   0.   0.000
CT2   CT   OH1  5 110.10   633.46   0.   0.000
OH1   CTCC  5 110.10   633.46   0.   0.000
CT   OH1 H  5 106.00   481.16   0.   0.000

[ dihedraltypes ]
HA   CT2CC   OC  9   180.00   0.2092 6
CT   CT2CC   OC  9   180.00   0.2092 6
CT2   CT   CT2   CC  9 0.00   4. 3
OH1   CT   CT2   CC  9 0.00   0.8368 3
OH1   CT   CT2   HA  9 0.00   0.8368 3
CCCT   CT2   CC  9 0.00   0.8368 3
CCCT   CT2   HA  9 0.00   0.8368 3
CT2   CT   CT2   HA  9 0.00   0.8368 3
OH1   CTCC   OC  9 0.00   1.2000 2
CT2   CTCC   OC  9   180.00   0.2092 6
CCCT   OH1H  9 0.00   0.2092 1
CT2   CT   OH1H  9 0.00   0.5858 3
CC   CT2OC   OC  2 0.00  803.328
CCCTOC   OC  2 0.00  803.328

[ moleculetype ]
CIT 3

[ atoms ]
1   CC   1  CIT   C  1   0.62012.011
2   CT2  1  CIT   C  2  -0.18012.011
3   CT   1  CIT   C  3  -0.07012.011
4   CC   1  CIT   C  4   0.62012.011
5   CT2  1  CIT   C  5  -0.18012.011
6   CC   1  CIT   C  6   0.62012.011
7   OC   1  CIT   O  7  -0.76015.999
8   OC   1  CIT   O  8  -0.76015.999
9   OC   1  CIT   O  9  -0.76015.999
10  OC   1  CIT   O 10  -0.76015.999
11  OC   1  CIT   O 11  -0.76015.999
12  OC   1  CIT   O 12  -0.76015.999
13  OH1  1  CIT   O 13  -0.54015.999
14  HA   1  CIT   H 14   0.090 1.008
15  HA   1  CIT   H 15   0.090 1.008
16  HA   1  CIT   H 16   0.090 1.008
17  HA   1  CIT   H 17   0.090 1.008
18  H1  CIT   H 18   0.310 1.008

[ bonds ]
1 81
1 71
1 2   1
2 15   1
2 14   1
2 31
3 13   1
3 51
3 41
4 10   1
4 91
5 17   1
5 16   1
5 61
6 12   1
6 11   1
13 18  1
[ angles ]
8 1 7   5
8 1 2   5
7 1 2   5
1 215   5
15214   5
152 3   5
1 214   5
142 3   5
1 2 3   5
2 313   5
133 5   5
133 4   5
2 3 5   5
5 3 4   5
2 3 4   5
3 410   5
104 9   5
3 4 9   5
3 517   5
17516   5
175 6   5
3 516   5
165 6   5
3 5 6   5
5 612   5
12611   5
5 611   5
31318   5

[ exclusions ]
18  9 10

[ pairs ]
10 18 2 0.3 -0.760 0.310 0.17145 0.310857
9  18 2 0.3 -0.760 0.310 0.17145 0.310857

[ dihedrals ]
812   15  9
712   15  9
812   14  9
712   14  9
8123  9
7123  9
123   13  9
15   23   13  9
14   23   13  9
1235  9
15   235  9
14   235  9
1234  9
15   234  9
14   234  9
23   13   18  9
53   13   18  9
43   13   18  9
235   17  9
13   35   17  9
435   17  9
235   16  9
13   35   16  9
435   16  9
2356  9
13   356  9
4356  9
234   10  9
13   34   10  9
534   10  9
2349  9
13   349  9
5349  9
356   12  9
17   56   12  9
16   56   12  9
356   11  9
17   56   11  9
16   56   11  9

[ dihedrals ]
1  2  7 8 2
4  3  9 102
6  5  11122

#ifdef POSRES_CITMolecule
[ position_restraints ]
; atom  type  fx  fy  fz
   1 1 1000 1000 1000
   2 1 1000 1000 1000
   3 1 1000 1000 1000
   4 1 1000 1000 1000
   5 1 1000 1000 1000
   6 1 1000 1000 1000
   7 1 1000 1000 1000
   8 1 1000 1000 1000
   9 1 1000 1000 1000
  10 1 1000 1000 1000
  

[gmx-users] Water model choice

[Pandya, Akash]

Hi all,

Which water model is best to use with the CHARMM27 FF, Tip3p or SPC/E?  I know 
the CHARMM FF has been optimised with Tip3p, but I also know that SPC/E water 
model has good agreement with experimental data e.g. diffusion coefficient.

Any guidance will be much appreciated?

Akash
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[gmx-users] Running gromacs analysis on a HPC

[Pandya, Akash]

Hi all,

I am trying to run gmx rdf on a HPC via a script. This is the command I am 
using :

echo 1 12 | gmx rdf -s proteinwater.tpr -f proteinwater.xtc -o 
proteinwaterrdf.xvg -bin 0.002 -norm rdf -selrpos whole_res_com

1 being the protein and 12 being the water


I get this error:

Program: gmx rdf, version 2018.2

Error in user input:
Invalid selection '1 12 '
  Near '12'
syntax error

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please can you advise me on how I can sort out this issue.


Akash
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[gmx-users] Density of ligand molecules around a particular residue

[Pandya, Akash]

Hi all,

I want to calculate the density of ligand molecules around a particular 
residue. Is there a gromacs tool that can achieve this? I've explored gmx 
spatial, gmx densmap but have had no luck. Any guidance will be much 
appreciated.

Akash
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[gmx-users] Error in generating a gromacs structure file for Arginine

[Pandya, Akash]

Hi all,

I'm trying to run MD simulations with Arginine. I'm using the AMBER99SB-ILDN FF 
and I get this error:

There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).

I've tried to search the error but don't know what I have done wrong? I used 
the command below:

gmx pdb2gmx -f Arg.pdb -o Arg.gro -water tip3p

The Arg.pdb looks like this:

COMPNDArginine
AUTHORGENERATED BY OPEN BABEL 2.3.90
ATOM  1  O   Arg A   1  -2.303  -1.954  -0.204  1.00  0.00   O
ATOM  2  OXT Arg A   1  -3.444  -0.531   1.147  1.00  0.00   O
ATOM  3  N   Arg A   1  -2.892   1.602  -0.334  1.00  0.00   N
ATOM  4  NE  Arg A   1   1.964  -0.236   0.050  1.00  0.00   N
ATOM  5  NH1 Arg A   1   3.918  -1.417  -0.350  1.00  0.00   N
ATOM  6  NH2 Arg A   1   4.137   0.763   0.281  1.00  0.00   N
ATOM  7  CB  Arg A   1  -0.770   0.493  -0.870  1.00  0.00   C
ATOM  8  CG  Arg A   1  -0.171   0.875   0.492  1.00  0.00   C
ATOM  9  CA  Arg A   1  -2.299   0.356  -0.813  1.00  0.00   C
ATOM 10  CD  Arg A   1   1.345   1.033   0.437  1.00  0.00   C
ATOM 11  C   Arg A   1  -2.746  -0.721   0.159  1.00  0.00   C
ATOM 12  CZ  Arg A   1   3.260  -0.263   0.006  1.00  0.00   C
ATOM 13  HB1 Arg A   1  -0.337  -0.454  -1.215  1.00  0.00   H
ATOM 14  HB2 Arg A   1  -0.499   1.254  -1.613  1.00  0.00   H
ATOM 15  HG1 Arg A   1  -0.595   1.821   0.847  1.00  0.00   H
ATOM 16  HG2 Arg A   1  -0.419   0.109   1.237  1.00  0.00   H
ATOM 17  HA  Arg A   1  -2.702   0.120  -1.804  1.00  0.00   H
ATOM 18  HD1 Arg A   1   1.601   1.820  -0.282  1.00  0.00   H
ATOM 19  HD2 Arg A   1   1.695   1.340   1.430  1.00  0.00   H
ATOM 20  H1  Arg A   1  -3.908   1.542  -0.388  1.00  0.00   H
ATOM 21  H2  Arg A   1  -2.621   2.369  -0.949  1.00  0.00   H
ATOM 22  H   Arg A   1  -2.603  -2.648   0.421  1.00  0.00   H
ATOM 23 HH11 Arg A   1   3.406  -2.261  -0.582  1.00  0.00   H
ATOM 24 HH12 Arg A   1   4.931  -1.459  -0.390  1.00  0.00   H
ATOM 25 HH21 Arg A   1   5.140   0.625   0.213  1.00  0.00   H
ATOM 26 HH22 Arg A   1   3.821   1.686   0.556  1.00  0.00   H

CONECT1   11   22
CONECT2   11
CONECT39   20   21
CONECT4   10   12
CONECT5   12   23   24
CONECT6   12   25   26
CONECT789   13   14
CONECT87   10   15   16
CONECT937   11   17
CONECT   1048   18   19
CONECT   11129
CONECT   12456
CONECT   137
CONECT   147
CONECT   158
CONECT   168
CONECT   179
CONECT   18   10
CONECT   19   10
CONECT   203
CONECT   213
CONECT   221
CONECT   235
CONECT   245
CONECT   256
CONECT   266
MASTER00000000   260   260
END

Please advise me on how to solve this error.


Akash
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[gmx-users] Topology for alphaketoglutarate to use in Gromacs

[Pandya, Akash]

Hi,

Can anyone guide me in generating Amber FF parameters for alphaketoglutarate to 
use in Gromacs? e.g. a tutorial?

Best wishes,

Akash


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[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I'm trying to work out how many molecules of ligand and water I have within a 
certain distance. I used the gmx select command below:

gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname 
LIG and within 0.5 of whole_res_com of resnr 1' -dt 100

However, this only outputs atomic positions. How can I get the number of "whole 
molecules"? If that makes sense? Or is there another command I can use?

Akash

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[gmx-users] SASA calculation

[Pandya, Akash]

Hi all,

I'm trying to calculate the SASA of my protein, however I am getting this 
warning message:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

How can I fix this?

Akash


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Re: [gmx-users] Citrate parameters

[Pandya, Akash]

Thank you Justin and Mark, it worked. I will bare all this in mind.

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Justin Lemkul
Sent: 12 April 2019 16:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters



On 4/12/19 11:57 AM, Pandya, Akash wrote:
> How would I find out if there are duplicates or not?

grompp has told you what it is finding as duplicates. You need to look into the 
parent force field files and compare the values you are supplying vs. what are 
in the existing force field, particularly for the atom types. grompp has 
already told you the existing (force field) and new (your topology) values.

-Justin

> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  On Behalf Of Mark 
> Abraham
> Sent: 12 April 2019 16:47
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Citrate parameters
>
> Hi,
>
> It seems that all/most things before the [moleculetype] definition duplicates 
> the standard contents of the forcefield, as you can see from the contents of 
> the itp file and the original warnings you mentioned.
> Unfortunately you now have the problem of determining whether all of it is 
> duplication, or only some of it.
>
> Mark
>
> On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
> 
> wrote:
>
>> Sorry but I don't quite understand where the duplicates come from?
>> I've pasted my itp file below:
>>
>> [ defaults ]
>> 1 2 yes 1.0 1.0
>>
>> [ atomtypes ]
>> OC  8 15. -0.760 A 0.302906 0.50208 CC  6 12.0110  0.620 A
>> 0.356359 0.29288 HA  1  1.0080  0.090 A 0.235197 0.09205
>> CT2 6 12.0110 -0.180 A 0.387541 0.23012 CT  6 12.0110 -0.070 A
>> 0.405359 0.08368
>> OH1 8 15. -0.540 A 0.315378 0.63639
>> H   1  1.0080  0.310 A 0.040001 0.19623
>>
>> [ bondtypes ]
>> CC OC  1  0.126 439320.0
>> CC CT2 1  0.152 167360.0
>> CT2HA  1  0.111 258571.2
>> OH1H   1  0.096 456056.0
>> CT CC  1  0.152 167360.0
>> CT2CT  1  0.150 186188.0
>> CT OH1 1  0.142 358150.4
>>
>> [ angletypes ]
>> OCCCOC  5 124.00   836.80   0.2225   58576.000
>> OCCC   CT2  5 118.00   334.72   0.2388   41840.000
>> CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>> HA   CT2HA  5 109.00   297.06   0.18024518.720
>> CTCCOC  5 118.00   334.72   0.2388   41840.000
>> CT2   CTCC  5 108.00   435.14   0.   0.000
>> CT2   CT   CT2  5 113.60   488.27   0.25619338.688
>> HA   CT2CT  5 110.10   279.74   0.2179   18853.104
>> CC   CT2CT  5 108.00   435.14   0.   0.000
>> CT2   CT   OH1  5 110.10   633.46   0.   0.000
>> OH1   CTCC  5 110.10   633.46   0.   0.000
>> CT   OH1 H  5 106.00   481.16   0.   0.000
>>
>> [ dihedraltypes ]
>> HA   CT2CC   OC  9   180.00   0.2092 6
>> CT   CT2CC   OC  9   180.00   0.2092 6
>> CT2   CT   CT2   CC  9 0.00   4. 3
>> OH1   CT   CT2   CC  9 0.00   0.8368 3
>> OH1   CT   CT2   HA  9 0.00   0.8368 3
>> CCCT   CT2   CC  9 0.00   0.8368 3
>> CCCT   CT2   HA  9 0.00   0.8368 3
>> CT2   CT   CT2   HA  9 0.00   0.8368 3
>> OH1   CTCC   OC  9 0.00   1.2000 2
>> CT2   CTCC   OC  9   180.00   0.2092 6
>> CCCT   OH1H  9 0.00   0.2092 1
>> CT2   CT   OH1H  9 0.00   0.5858 3
>> CC   CT2OC   OC  2 0.00  803.328
>> CCCTOC   OC  2 0.00  803.328
>>
>> [ moleculetype ]
>> CIT 3
>>
>> [ atoms ]
>> 1   CC   1  CIT   C  1   0.62012.011
>> 2   CT2  1  CIT   C  2  -0.18012.011
>> 3   CT   1  CIT   C  3  -0.07012.011
>> 4   CC   1  CIT   C  4   0.62012.011
>> 5   CT2  1  CIT   C  5  -0.18012.011
>> 6   CC   1  CIT   C  6   0.62012.011
>> 7   OC   1  CIT   O  7  -0.76015.999
>> 8   OC   1  CIT   O  8  -0.76015.999
>> 9   OC   1  CIT   O  9  -0.76015.999
>> 10  OC   1  CIT   O 10  -0.76015.999
>> 11  OC   1  CIT   O 11  -0.76015.999
>> 12  OC   1  CIT   O 12  -0.76015.999
>> 13  OH1  1  CIT   O 13  -0.54015.999
>> 14  HA   1  CIT   H 14   0.090 1.008
>> 15  HA   1  CIT   H 15   0.090 1.008
>> 16  HA   1  CIT   H 16   0.090 1.008
>> 17  HA   1  CIT   H 17   0.090 1.008
>> 18  H1  CIT   H 18   0.310 1.008
>>
>> [ bonds ]
>> 1 81
>> 1 71
>> 1 2   1
>> 2 15   1
>> 2 14   1
>> 2 31
>> 3 13   1
>> 3 5

Re: [gmx-users] Citrate parameters

[Pandya, Akash]

How would I find out if there are duplicates or not? 

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Mark Abraham
Sent: 12 April 2019 16:47
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Citrate parameters

Hi,

It seems that all/most things before the [moleculetype] definition duplicates 
the standard contents of the forcefield, as you can see from the contents of 
the itp file and the original warnings you mentioned.
Unfortunately you now have the problem of determining whether all of it is 
duplication, or only some of it.

Mark

On Fri., 12 Apr. 2019, 17:39 Pandya, Akash, 
wrote:

> Sorry but I don't quite understand where the duplicates come from? 
> I've pasted my itp file below:
>
> [ defaults ]
> 1 2 yes 1.0 1.0
>
> [ atomtypes ]
> OC  8 15. -0.760 A 0.302906 0.50208 CC  6 12.0110  0.620 A 
> 0.356359 0.29288 HA  1  1.0080  0.090 A 0.235197 0.09205
> CT2 6 12.0110 -0.180 A 0.387541 0.23012 CT  6 12.0110 -0.070 A 
> 0.405359 0.08368
> OH1 8 15. -0.540 A 0.315378 0.63639
> H   1  1.0080  0.310 A 0.040001 0.19623
>
> [ bondtypes ]
> CC OC  1  0.126 439320.0
> CC CT2 1  0.152 167360.0
> CT2HA  1  0.111 258571.2
> OH1H   1  0.096 456056.0
> CT CC  1  0.152 167360.0
> CT2CT  1  0.150 186188.0
> CT OH1 1  0.142 358150.4
>
> [ angletypes ]
> OCCCOC  5 124.00   836.80   0.2225   58576.000
> OCCC   CT2  5 118.00   334.72   0.2388   41840.000
> CC   CT2HA  5 109.50   276.14   0.2163   25104.000
> HA   CT2HA  5 109.00   297.06   0.18024518.720
> CTCCOC  5 118.00   334.72   0.2388   41840.000
> CT2   CTCC  5 108.00   435.14   0.   0.000
> CT2   CT   CT2  5 113.60   488.27   0.25619338.688
> HA   CT2CT  5 110.10   279.74   0.2179   18853.104
> CC   CT2CT  5 108.00   435.14   0.   0.000
> CT2   CT   OH1  5 110.10   633.46   0.   0.000
> OH1   CTCC  5 110.10   633.46   0.   0.000
> CT   OH1 H  5 106.00   481.16   0.   0.000
>
> [ dihedraltypes ]
> HA   CT2CC   OC  9   180.00   0.2092 6
> CT   CT2CC   OC  9   180.00   0.2092 6
> CT2   CT   CT2   CC  9 0.00   4. 3
> OH1   CT   CT2   CC  9 0.00   0.8368 3
> OH1   CT   CT2   HA  9 0.00   0.8368 3
> CCCT   CT2   CC  9 0.00   0.8368 3
> CCCT   CT2   HA  9 0.00   0.8368 3
> CT2   CT   CT2   HA  9 0.00   0.8368 3
> OH1   CTCC   OC  9 0.00   1.2000 2
> CT2   CTCC   OC  9   180.00   0.2092 6
> CCCT   OH1H  9 0.00   0.2092 1
> CT2   CT   OH1H  9 0.00   0.5858 3
> CC   CT2OC   OC  2 0.00  803.328
> CCCTOC   OC  2 0.00  803.328
>
> [ moleculetype ]
> CIT 3
>
> [ atoms ]
> 1   CC   1  CIT   C  1   0.62012.011
> 2   CT2  1  CIT   C  2  -0.18012.011
> 3   CT   1  CIT   C  3  -0.07012.011
> 4   CC   1  CIT   C  4   0.62012.011
> 5   CT2  1  CIT   C  5  -0.18012.011
> 6   CC   1  CIT   C  6   0.62012.011
> 7   OC   1  CIT   O  7  -0.76015.999
> 8   OC   1  CIT   O  8  -0.76015.999
> 9   OC   1  CIT   O  9  -0.76015.999
> 10  OC   1  CIT   O 10  -0.76015.999
> 11  OC   1  CIT   O 11  -0.76015.999
> 12  OC   1  CIT   O 12  -0.76015.999
> 13  OH1  1  CIT   O 13  -0.54015.999
> 14  HA   1  CIT   H 14   0.090 1.008
> 15  HA   1  CIT   H 15   0.090 1.008
> 16  HA   1  CIT   H 16   0.090 1.008
> 17  HA   1  CIT   H 17   0.090 1.008
> 18  H1  CIT   H 18   0.310 1.008
>
> [ bonds ]
> 1 81
> 1 71
> 1 2   1
> 2 15   1
> 2 14   1
> 2 31
> 3 13   1
> 3 51
> 3 41
> 4 10   1
> 4 91
> 5 17   1
> 5 16   1
> 5 61
> 6 12   1
> 6 11   1
> 13 18  1
> [ angles ]
> 8 1 7   5
> 8 1 2   5
> 7 1 2   5
> 1 215   5
> 15214   5
> 152 3   5
> 1 214   5
> 142 3   5
> 1 2 3   5
> 2 313   5
> 133 5   5
> 133 4   5
> 2 3 5   5
> 5 3 4   5
> 2 3 4   5
> 3 410   5
> 104 9   5
> 3 4 9   5
> 3 517   5
> 17516   5
> 175 6   5
> 3 516   5
> 165 6   5
> 3 5 6   5
> 5 612   5
> 12611   5
> 5 611   5
> 31318   5
>
> [ exclusions ]
> 18  9 10
>
> [ pairs ]
> 10 18 2 0.3 -0.760 0.310 0.17145 0.310857
> 9  18 2 0.3 -0.760 0.310 0.17145 0.310857
>
> [ dihedrals ]
> 812   15  9
> 712   15  9
> 812   14  9
> 712   14  9
> 8123  9
> 712

Re: [gmx-users] Citrate parameters

[Pandya, Akash]

 Of Justin Lemkul
Sent: 12 April 2019 16:14
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters



On 4/12/19 10:52 AM, Pandya, Akash wrote:
> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the system, I 
> get this error. Can anybody help with this?

Your citrate topology is introducing duplicate parameters that already exist in 
the force field. In this instance, they appear to be exact copies (at least for 
the bonded parameters shown) but this is bad practice. Eliminate the 
redundancies.

-Justin

> WARNING 1 [file CITff.itp, line 3]:
>Overriding atomtype OC
>
>
> WARNING 2 [file CITff.itp, line 4]:
>Overriding atomtype CC
>
>
> WARNING 3 [file CITff.itp, line 5]:
>Overriding atomtype HA
>
>
> WARNING 4 [file CITff.itp, line 6]:
>Overriding atomtype CT2
>
>
> WARNING 5 [file CITff.itp, line 7]:
>Overriding atomtype CT
>
>
> WARNING 6 [file CITff.itp, line 8]:
>Overriding atomtype OH1
>
>
> WARNING 7 [file CITff.itp, line 9]:
>Overriding atomtype H
>
>
> WARNING 8 [file CITff.itp, line 13]:
>Overriding Bond parameters.
>
>old:  0.1522 167360 0.1522 167360
>new: CC CT2 1  0.152 167360.0
>
>
> WARNING 9 [file CITff.itp, line 14]:
>Overriding Bond parameters.
>
>old:  0. 258571 0. 258571
>new: CT2HA  1  0.111 258571.2
>
>
> WARNING 10 [file CITff.itp, line 23]:
>Overriding U-B parameters.
>
>old:  109.5 276.144 0.2163 25104 
> 109.5 276.144 0.2163 25104
>new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>
>
> WARNING 11 [file CITff.itp, line 24]:
>Overriding U-B parameters.
>
>old:  109 297.064 0.1802 4518.72 
> 109 297.064 0.1802 4518.72
>new: HA   CT2HA  5 109.00   297.06   0.18024518.720
>
> Generated 20503 of the 20503 non-bonded parameter combinations 
> Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 
> 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 
> 'Protein_chain_H'
> Excluding 3 bonded neighbours molecule type 'CIT'
> Excluding 3 bonded neighbours molecule type 'GLY'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 62703]:
>System has non-zero total charge: -46.95
>Total charge should normally be an integer. See
>
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FFloating_Point_Arithmeticdata=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906788597905747sdata=oxvEKXN67Oq%2B2F2Wm4WQ0uPCtOZxTVsn%2Fv9hiF%2FGeCI%3Dreserved=0
>for discussion on how close it should be to an integer.
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet Analysing 
> residue names:
> There are:  1366Protein residues
> There are:23  Other residues
> There are: 56714  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
> groups...
> Number of degrees of freedom in T-Coupling group rest is 389088.00 
> Calculating fourier grid dimensions for X Y Z Using a fourier grid of 
> 104x104x104, spacing 0.120 0.120 0.120 Estimate for the relative 
> computational load of the PME mesh part: 0.19 This run will generate 
> roughly 14 Mb of data
>
> There were 2 notes
>
> There were 11 warnings
>
> ---
> Program: gmx grompp, version 2016.2
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)
>
> Fatal error:
> Too many warnings (11).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the 
> GROMACS website at 
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g
> romacs.org%2FDocumentation%2FErrorsdata=02%7C01%7Cakash.pandya.15
> %40ucl.ac.uk%7C4504ba31ee1b4063a30d08d6bf59885e%7C1faf88fea9984c5b93c9
> 210a11d9a5c2%7C0%7C0%7C636906788597905747sdata=WGY4ht%2BgVmeJ3bJX
> YAg5Y7ciNSUk3MhMwkbnSnob%2F0I%3Dreserved=0
>

--
==

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
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Re: [gmx-users] Citrate parameters

[Pandya, Akash]

I'm using the CHARMM27 FF and I obtained the parameters from literature.

Akash 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Soham Sarkar
Sent: 12 April 2019 16:05
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters

Which force field you are using and how you made the itp of the citrate 
molecule?

On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash, 
wrote:

> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the 
> system, I get this error. Can anybody help with this?
>
> WARNING 1 [file CITff.itp, line 3]:
>   Overriding atomtype OC
>
>
> WARNING 2 [file CITff.itp, line 4]:
>   Overriding atomtype CC
>
>
> WARNING 3 [file CITff.itp, line 5]:
>   Overriding atomtype HA
>
>
> WARNING 4 [file CITff.itp, line 6]:
>   Overriding atomtype CT2
>
>
> WARNING 5 [file CITff.itp, line 7]:
>   Overriding atomtype CT
>
>
> WARNING 6 [file CITff.itp, line 8]:
>   Overriding atomtype OH1
>
>
> WARNING 7 [file CITff.itp, line 9]:
>   Overriding atomtype H
>
>
> WARNING 8 [file CITff.itp, line 13]:
>   Overriding Bond parameters.
>
>   old:  0.1522 167360 0.1522 167360
>   new: CC CT2 1  0.152 167360.0
>
>
> WARNING 9 [file CITff.itp, line 14]:
>   Overriding Bond parameters.
>
>   old:  0. 258571 0. 258571
>   new: CT2HA  1  0.111 258571.2
>
>
> WARNING 10 [file CITff.itp, line 23]:
>   Overriding U-B parameters.
>
>   old:  109.5 276.144 0.2163 25104
> 109.5 276.144 0.2163 25104
>   new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000
>
>
> WARNING 11 [file CITff.itp, line 24]:
>   Overriding U-B parameters.
>
>   old:  109 297.064 0.1802 4518.72
> 109 297.064 0.1802 4518.72
>   new: HA   CT2HA  5 109.00   297.06   0.18024518.720
>
> Generated 20503 of the 20503 non-bonded parameter combinations 
> Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 
> 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 
> 'Protein_chain_H'
> Excluding 3 bonded neighbours molecule type 'CIT'
> Excluding 3 bonded neighbours molecule type 'GLY'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 62703]:
>   System has non-zero total charge: -46.95
>   Total charge should normally be an integer. See
>   
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FFloating_Point_Arithmeticdata=02%7C01%7Cakash.pandya.15%40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=mMSRKLOaTcASmbpt%2BVctQztiZY%2F6xpgswsGtQUIrI5s%3Dreserved=0
>   for discussion on how close it should be to an integer.
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet Analysing 
> residue names:
> There are:  1366Protein residues
> There are:23  Other residues
> There are: 56714  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and 
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 389088.00 
> Calculating fourier grid dimensions for X Y Z Using a fourier grid of 
> 104x104x104, spacing 0.120 0.120 0.120 Estimate for the relative 
> computational load of the PME mesh part: 0.19 This run will generate 
> roughly 14 Mb of data
>
> There were 2 notes
>
> There were 11 warnings
>
> ---
> Program: gmx grompp, version 2016.2
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)
>
> Fatal error:
> Too many warnings (11).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the 
> GROMACS website at 
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g
> romacs.org%2FDocumentation%2FErrorsdata=02%7C01%7Cakash.pandya.15
> %40ucl.ac.uk%7Ce8508f4823794c31f19b08d6bf586181%7C1faf88fea9984c5b93c9
> 210a11d9a5c2%7C0%7C0%7C636906783645721595sdata=dF0uRrtoKsq3K9uJyL
> w60UZo3bwuWC4%2BYlMGrBRzaDA%3Dreserved=0
>
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[gmx-users] Citrate parameters

[Pandya, Akash]

Hi all,

My simulation contains citrate molecules. When I try to solvate the system, I 
get this error. Can anybody help with this?

WARNING 1 [file CITff.itp, line 3]:
  Overriding atomtype OC


WARNING 2 [file CITff.itp, line 4]:
  Overriding atomtype CC


WARNING 3 [file CITff.itp, line 5]:
  Overriding atomtype HA


WARNING 4 [file CITff.itp, line 6]:
  Overriding atomtype CT2


WARNING 5 [file CITff.itp, line 7]:
  Overriding atomtype CT


WARNING 6 [file CITff.itp, line 8]:
  Overriding atomtype OH1


WARNING 7 [file CITff.itp, line 9]:
  Overriding atomtype H


WARNING 8 [file CITff.itp, line 13]:
  Overriding Bond parameters.

  old:  0.1522 167360 0.1522 167360
  new: CC CT2 1  0.152 167360.0


WARNING 9 [file CITff.itp, line 14]:
  Overriding Bond parameters.

  old:  0. 258571 0. 258571
  new: CT2HA  1  0.111 258571.2


WARNING 10 [file CITff.itp, line 23]:
  Overriding U-B parameters.

  old:  109.5 276.144 0.2163 25104 
109.5 276.144 0.2163 25104
  new: CC   CT2HA  5 109.50   276.14   0.2163   25104.000


WARNING 11 [file CITff.itp, line 24]:
  Overriding U-B parameters.

  old:  109 297.064 0.1802 4518.72 109 
297.064 0.1802 4518.72
  new: HA   CT2HA  5 109.00   297.06   0.18024518.720

Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_H'
Excluding 3 bonded neighbours molecule type 'CIT'
Excluding 3 bonded neighbours molecule type 'GLY'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 62703]:
  System has non-zero total charge: -46.95
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  1366Protein residues
There are:23  Other residues
There are: 56714  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 389088.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 104x104x104, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.19
This run will generate roughly 14 Mb of data

There were 2 notes

There were 11 warnings

---
Program: gmx grompp, version 2016.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)

Fatal error:
Too many warnings (11).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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[gmx-users] Pairwise distances from COM of residues

[Pandya, Akash]

Hi all,


My protein is 168 amino acid residues long. I want to calculate the pairwise 
distance between the COM of each individual residue and my ligand molecules 
during my trajectory. As I have 168 amino acids, this will take ages if I run 
the gmx pairdist code each time. I was wondering whether there is a way to run 
this calculation via a script in gromacs?


Akash
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[gmx-users] Generating parameters of Alpha-Ketoglutarate for AMBER FF

[Pandya, Akash]

Hi all,

I am simulating my protein with Alpha-Ketoglutarate and I have been searching 
literature on ways to parameterise the molecule for the AMBER FF. I'm not 
having any luck and was wondering if anyone has or knows how to parameterise 
Alpha-Ketoglutarate? The chemical formula is C5H4O5-2.

Any guidance will be much appreciated.

Akash
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[gmx-users] gmx select help

[Pandya, Akash]

Hi all,

I am running the gmx select command to create a file with all my ligand 
molecules that are within  the cut-off distance specified from the COM of a 
protein residue as a function of time. Here is the command I am using:


gmx select -f traj2.gro -s protein.tpr -dt 100 -on index.ndx -select 'resname 
LIG and within 0.5 of res_com of resnr 183' -resnr number


The file currently outputs atom numbers for my ligand molecules. If I only 
wanted the resid of my ligands (as named in the trajectory file, e.g. resid 130 
LIG) instead of the atom id  to be written, how would I do this?

Akash

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[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I am running the gmx select command to obtain all my ligand molecules that are 
within a cut-off distance from the COM of a protein residue as a function of 
time. The output from the command below comes with just the atom positions of 
my ligand.


gmx select -f protein_gly.gro -s protein.tpr -n mindist1.ndx -dt 100 -oi 
index.dat -select 'resname LIG and within 3 of res_com of resnr 183' -resnr 
index


Is there a way to only output the residue number instead of the atom numbers?

Akash
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[gmx-users] Minimum distance of ligand molecules

[Pandya, Akash]

Hi all,


For example if I have 200 ligand molecules in my system, is there a way of 
plotting the identity of those ligands in the form of an index (e.g. 1,2,3, 
etc...) with minimum distance from the binding sites as function of time?


Akash

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[gmx-users] Plotting ligand index number corresponding to minimum distance data

[Pandya, Akash]

Hi all,

I have multiple ligands in my system. I have calculated the minimum distance 
between the COM of my binding site and the ligand molecules. I was wondering if 
there was a way I can also include a second Y axis showing the ligand index 
number corresponding to the minimum distance data. The aim is to identify the 
ligand molecules that maybe "visiting" the binding site during the course of 
the simulation.

I hope that makes sense and someone will be able to help me.


Thanks in advance,

Akash
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[gmx-users] Total time of ligand in active site

[Pandya, Akash]

Hi all,

I wanted to find out if there was a way of calculating the total time a ligand 
was present in the active site during the MD simulation?


Many thanks,

Akash
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[gmx-users] PCA and Fast Fourier Transform

[Pandya, Akash]

Hi all,

I have carried out PCA on my MD trajectories. I want to investigate the 
frequency distribution of my MD trajectory projected on Principle Component 
modes (PC1, PC2 etc.). I ultimately want these frequencies as function of time 
using Fourier Transform. Is there any Gromacs utility that can facilitate this?


Many thanks,

Akash
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[gmx-users] gmx clustsize

[Pandya, Akash]

Hi all,

I am trying to find out how many clusters I have of my ligand during the course 
of my trajectory using gmx clustsize.

I type the following command and get an error message:


gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc histo-clust.xvg 
-mol




Program: gmx clustsize, version 2016.2
Source file: src/gromacs/fileio/matio.cpp (line 690)

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Could anyone help me with this problem? I know for a fact that I don't just 
have one cluster of glycine (by inspection).

Thank you,

Akash

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[gmx-users] Cluster analysis on molecules

[Pandya, Akash]

Hi all,

I want to calculate the number of clusters of my glycine molecules during the 
course of my simulation. I have read that gmx clustsize is the correct command 
to use. I read on one of the previous threads that I will have to create a 
separate tpr file for the molecules of interest. I also stripped the original 
trajectory to make a new one with glycine molecules only. I run the command 
below:


gmx clustsize -f glycine.gro -s glycine.tpr -nc nclust.xvg -mol


I get an error message saying that gromacs only finds 1 cluster but this is 
contradictory to what I am seeing when I viewed the trajectory.


Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

Can somebody please advise me on how to overcome this issue?


Many thanks,

Akash

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[gmx-users] Extending MD simulations

[Pandya, Akash]

Hi all,

I tried extending my MD simulation from 60 ns to 100 ns with the following 
commands:

gmx convert-tpr -s md_0_1.tpr -extend 4 -o new.tpr

gmx mdrun_mpi  -deffnm new  -cpi md_0_1.cpt   -append


It seems to create new trajectory and log files each time starting from t =0 
and not from 6 ps. How do I fix this issue so that I just have one single 
log file and trajectory file?

Akash

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[gmx-users] Selection Error for RDF calculations

[Pandya, Akash]

Hi all,

I am trying to calculate the RDF in system with my protein and also glycine. I 
have made a custom index groups for the protein and also the glycine as show 
below:


> ri 1-442

Found 6615 atoms with resind.+1 in range 1-442

24 r_1-442 :  6615 atoms

> ri 466-619

Found 1540 atoms with resind.+1 in range 466-619

25 r_466-619   :  1540 atoms


When I type in the appropriate command:

gmx rdf -f protein_gly.gro -n protein_gly.ndx -b 0 -e 6 -tu ns -o rdf.xvg 
-norm rdf -bin 0.2



I get the following error when I finish selecting the 'ref' which is the 
protein and `sel` which is the glycine molecules


Inconsistency in user input:
Invalid index group references encountered
  Group 'r_466-619' cannot be used in selections, because it contains negative
  atom indices and/or references atoms not present (largest allowed atom index
  is 8155).

Please can someone advise me on what I should do?

Akash

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[gmx-users] Handling Periodic Boundary Conditions

[Pandya, Akash]

Hi all,

I'm having trouble with visualisation of my system after the MD production run. 
I have tried the periodic boundary conditions workflow suggested on the gromacs 
website, although I'm having no luck. I have used the following command to try 
and obtain a visualisation state that I can work with.

gmx trjconv -f Nonwater.xtc -s non_water.tpr -pbc whole -center -o nonwater.gro

When I visualised this trajectory, my protein molecule appears to have split 
even though I used -pbc whole. Can someone please help me overcome this issue?

Many thanks,

Akash
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Re: [gmx-users] Running MD simulations at a particular temperature

[Pandya, Akash]

So I equilibrated my system at 338.15 K , do I still need to use the simulated 
annealing option to maintain that temperature? My NPT mdp file is shown below.

title   = CHARMM27 A33FabGLY NPT equilibration 
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every  0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT 
constraint_algorithm = lincs; holonomic constraints 
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing = 0.16   ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; Nose-Hoover thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 338.15338.15  ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


Akash 
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 17 October 2017 10:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular temperature

Hi,

That's your question as part of your experimental design. Why do you want to do 
simulated annealing?

Mark

On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Is simulated annealing carried out during NPT or in the production run?
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
> Lemkul
> Sent: 20 September 2017 03:20
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Running MD simulations at a particular 
> temperature
>
>
>
> On 9/19/17 4:25 PM, Pandya, Akash wrote:
> > Hi all,
> >
> > I want to run my MD simulation at 65 degrees Celsius. The mdp file 
> > has a
> field as shown below:
> >
> > ref_t= 338.15  338.15 ; reference
> temperature, one for each group, in K
> >
> > I am wondering whether the simulation has already reached the 
> > desired
> temperature or does it heat up to 65 degrees throughout the course of 
> the simulation? I hope this makes sense.
>
> The answer depends on what you're doing.  If you've set "gen-vel = yes"
> and "gen-temp = 338.15" then you are initializing a simulation with 
> random velocities according to a Maxwell distribution at that 
> temperature. If your system is at some other temperature and you're 
> just trying to use a thermostat to force a change in that temperature, 
> there's no real "warming"
> going on, rather the thermostat is going to push the velocity 
> distribution towards the desired temperature.  Warming a system is 
> done via simulated annealing options.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://

Re: [gmx-users] Running MD simulations at a particular temperature

[Pandya, Akash]

Is simulated annealing carried out during NPT or in the production run?

Akash 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 20 September 2017 03:20
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular temperature



On 9/19/17 4:25 PM, Pandya, Akash wrote:
> Hi all,
>
> I want to run my MD simulation at 65 degrees Celsius. The mdp file has a 
> field as shown below:
>
> ref_t= 338.15  338.15 ; reference 
> temperature, one for each group, in K
>
> I am wondering whether the simulation has already reached the desired 
> temperature or does it heat up to 65 degrees throughout the course of the 
> simulation? I hope this makes sense.

The answer depends on what you're doing.  If you've set "gen-vel = yes" 
and "gen-temp = 338.15" then you are initializing a simulation with random 
velocities according to a Maxwell distribution at that temperature. If your 
system is at some other temperature and you're just trying to use a thermostat 
to force a change in that temperature, there's no real "warming" going on, 
rather the thermostat is going to push the velocity distribution towards the 
desired temperature.  Warming a system is done via simulated annealing options.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Running MD simulations at a particular temperature

[Pandya, Akash]

Hi all,

I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field 
as shown below:

ref_t= 338.15  338.15 ; reference 
temperature, one for each group, in K

I am wondering whether the simulation has already reached the desired 
temperature or does it heat up to 65 degrees throughout the course of the 
simulation? I hope this makes sense.

Many thanks,

Akash
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[gmx-users] Clustering

[Pandya, Akash]

Hi all,

I want to calculate the number of clusters of my glycine molecules during the 
course of my simulation. I have read that gmx clustsize is the correct command 
to use. I read on one of the previous threads that I will have create a 
separate tpr file for the molecule of interest. And I had to generate another 
trajectory file in order for them to match.  I run the command below:


gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 6 -cut 
0.35 -mol


I get an error message saying that gromacs only finds 1 cluster but this cannot 
be right as I can see more than one cluster forming during the simulation


Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

Can somebody please advise me on how to overcome this issue?


Many thanks,

Akash

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[gmx-users] Number of Clusters during my simulation

[Pandya, Akash]

Hi all,

I want to calculate the number of clusters of my glycine molecules during the 
course of my simulation. I have read that gmx clustsize is the correct command 
to use. I read on one of the previous threads that I will have create a 
separate tpr file for the molecule of interest. And I had to generate another 
trajectory file in order for them to match.  I run the command below:


gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 6 -cut 
0.35 -mol


I get an error message saying that gromacs only finds 1 cluster but this cannot 
be right as I see more than one cluster forming during the simulation


Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

Can somebody please advise me on how to overcome this issue?


Many thanks,

Akash
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[gmx-users] RDF Values

[Pandya, Akash]

Hi all,

I am calculating the RDF from a particular residue to a particular glycine 
molecule. I created an index file for both to do this. My simulation box is 
1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my 
trajectory and all the components stay inside the box. Please could someone 
tell me how to overcome this issue? My command line is below:

gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 6 -ref 
-sel -bin 0.5 -norm rdf


Akash
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Re: [gmx-users] gmx select

[Pandya, Akash]

So I tried with both opening and closing. It seems to select all the molecules 
in my box which is not what I want. I only want certain glycine molecules that 
are closest to the protein. May you please suggest another way is which I could 
achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname 
Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb 

Akash


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 13 July 2017 14:01
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select



On 7/13/17 3:38 AM, Pandya, Akash wrote:
> gmx select -f output.gro -select "Close to protein" resname Glyci and within 
> 0.5 of group "Protein"'
> 

I suspect Mark is right, this is an invalid command, because you have a closing 
' without an opening ' in your -select argument.  This should fail with a 
generic error message that the selection can't be parsed.  I am also curious 
about "resname Glyci" because if that's the case, then you must have hacked 
some force field files, because everyone calls glycine "GLY" per standard 
nomenclature.

-Justin

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Mark Abraham
> Sent: 13 July 2017 00:04
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
> 
> Hi,
> 
> Can you please copy, paste and post your actual commands. I don't think your 
> use of quote marks would have led to a valid shell command. The whole 
> selection text will need to be inside some quotes.
> 
> Mark
> 
> On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
> 
>> I have used the same name in my coordinate file. For Glycine it is 
>> spelt as Glyci, so the word has been cut off. I know this is correct 
>> because I use the same name in VMD.
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
>> Abraham
>> Sent: 12 July 2017 22:42
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] gmx select
>>
>> Hi,
>>
>> What are the residue names in your coordinate file? Glyci probably 
>> doesn't fit
>>
>> Mark
>>
>> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
>> <akash.pandya...@ucl.ac.uk>
>> wrote:
>>
>>> Hi all,
>>>
>>>
>>> I am trying to select all the glycine molecules with 0.5nm of my protein.
>>> I tried both of these commands I got from the gromacs website:
>>>
>>> gmx select -f output.gro -select "Close to protein" resname Glyci 
>>> and within 0.5 of group "Protein"' -ofpdb
>>>
>>> gmx select -f output.xtc -s output.tpr (my converted input file) 
>>> -select "Close to protein" resname Glyci and within 0.5 of group 
>>> "Protein"' -ofpdb
>>>
>>>
>>> Nothing comes up when I enter them. Please could someone help me 
>>> with
>> this?
>>>
>>>
>>> Akash
>>> --
>>> Gromacs Users mailing list
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>>>
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Re: [gmx-users] gmx select

[Pandya, Akash]

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 13 July 2017 00:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your 
use of quote marks would have led to a valid shell command. The whole selection 
text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> I have used the same name in my coordinate file. For Glycine it is 
> spelt as Glyci, so the word has been cut off. I know this is correct 
> because I use the same name in VMD.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 12 July 2017 22:42
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably 
> doesn't fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
> <akash.pandya...@ucl.ac.uk>
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci 
> > and within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file) 
> > -select "Close to protein" resname Glyci and within 0.5 of group 
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me 
> > with
> this?
> >
> >
> > Akash
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > posting!
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> > or send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] gmx select

[Pandya, Akash]

I have used the same name in my coordinate file. For Glycine it is spelt as 
Glyci, so the word has been cut off. I know this is correct because I use the 
same name in VMD.   

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 12 July 2017 22:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

What are the residue names in your coordinate file? Glyci probably doesn't fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Hi all,
>
>
> I am trying to select all the glycine molecules with 0.5nm of my protein.
> I tried both of these commands I got from the gromacs website:
>
> gmx select -f output.gro -select "Close to protein" resname Glyci and 
> within 0.5 of group "Protein"' -ofpdb
>
> gmx select -f output.xtc -s output.tpr (my converted input file) 
> -select "Close to protein" resname Glyci and within 0.5 of group 
> "Protein"' -ofpdb
>
>
> Nothing comes up when I enter them. Please could someone help me with this?
>
>
> Akash
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] gmx select

[Pandya, Akash]

Hi all,


I am trying to select all the glycine molecules with 0.5nm of my protein. I 
tried both of these commands I got from the gromacs website:

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"' -ofpdb

gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close 
to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb


Nothing comes up when I enter them. Please could someone help me with this?


Akash
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Re: [gmx-users] RDF

[Pandya, Akash]

When I try to make an index group for the protein residue and the ligand 
molecule, the whole system is included in the index file. 

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q

Akash 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 11 July 2017 18:06
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] RDF



On 7/11/17 11:41 AM, Pandya, Akash wrote:
> Hi,
> 
> I want to calculate the RDF between a specific residue and a ligand molecule 
> in my simulation box. Is this possible and do I have to make a special index 
> group for that? If so how would I go about doing that?
> 

By using make_ndx or a suitable command-line selection when running gmx rdf 
(see gmx help selections, but make_ndx is often much easier to use/comprehend 
for very simple cases like this).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] RDF

[Pandya, Akash]

Hi,

I want to calculate the RDF between a specific residue and a ligand molecule in 
my simulation box. Is this possible and do I have to make a special index group 
for that? If so how would I go about doing that?


Thanks,

Akash
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[gmx-users] Interpretation of MSD

[Pandya, Akash]

Hi all,

I performed Mean Square Deviation for my ligand molecules in x, y, z directions 
in order to obtain the diffusion coefficients. From my understanding, the 
square root of the highest MSD value should be significant enough to interpret 
that the ligand molecules have in fact moved enough during the course of the 
simulation. This may seem like an ambiguous question, but what would you deem a 
suitable value for MSD, for diffusion coefficients to be appropriate to measure?

Many thanks,

Akash
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

I want to see the closest binding glycine molecules so would "within x distance 
of any protein atom" be more appropriate?

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 28 June 2017 15:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

You get to choose... do you want everything within some distance of the protein 
center of mass, or any protein atom, or something else. But don't be suprrised 
if there are no ligand atoms super close to the protein center of mass ;-)

Mark

On Wed, Jun 28, 2017 at 12:47 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> I assumed it meant to select all ligand molecules closest to the 
> protein's centre of mass. I'm not entirely sure if that is correct 
> interpretation.
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 28 June 2017 11:34
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> How are you interpreting "within 4A of my protein?" What has your 
> protein's center of mass got to do with it?
>
> Mark
>
> On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash 
> <akash.pandya...@ucl.ac.uk>
> wrote:
>
> > Yes it is. So that means I need a cut-off greater than right?
> >
> > Akash
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> > Abraham
> > Sent: 28 June 2017 11:08
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> >
> > Is the radius of your protein greater than 0.4 nm?
> >
> > Mark
> >
> > On Wed, 28 Jun 2017 12:05 Pandya, Akash <akash.pandya...@ucl.ac.uk>
> wrote:
> >
> > > Hi,
> > >
> > > I want to select all the ligands in my box within 4A of my protein.
> > > I looked at gmx help select and I used the command below but 
> > > nothing appeared. It didn't show my default groups which 
> > > correspond to the "14" for ligand and "1" for protein. Please advise me 
> > > on what to do?
> > > Am I missing something?
> > >
> > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select 
> > > `group "14" and within 0.4 of com of group "1"'
> > >
> > > Many thanks,
> > >
> > > Akash
> > >
> > > -Original Message-
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
> > > Mark Abraham
> > > Sent: 21 June 2017 11:56
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> > >
> > > Hi,
> > >
> > > You aren't getting output because you aren't actually making a 
> > > selection - see "gmx help select" and its suggestions for where to 
> > > look for the rest of the documentation and explained examples.
> > >
> > > Mark
> > >
> > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash 
> > > <akash.pandya...@ucl.ac.uk>
> > > wrote:
> > >
> > > > I'm not sure if the command I entered (shown below) is correct. 
> > > > No output was given. I'm unclear as to how this command will 
> > > > enable me to isolate the glycine molecules within 4A of the 
> > > > protein
> molecule?
> > > >
> > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos 
> > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all
> > > >
> > > > Akash
> > > >
> > > > -Original Message-
> > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
> > > > Mark Abraham
> > > > Sent: 16 June 2017 17:22
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> > > >
> > > > Hi,
> > > >
> > > > Gmx select will produce a selection eg of all molecules with an 
> > > > atom within a cutoff of any atom in another molecule.
> > > >
> > > >

Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

I assumed it meant to select all ligand molecules closest to the protein's 
centre of mass. I'm not entirely sure if that is correct interpretation.

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 28 June 2017 11:34
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

How are you interpreting "within 4A of my protein?" What has your protein's 
center of mass got to do with it?

Mark

On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Yes it is. So that means I need a cut-off greater than right?
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 28 June 2017 11:08
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> Is the radius of your protein greater than 0.4 nm?
>
> Mark
>
> On Wed, 28 Jun 2017 12:05 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
>
> > Hi,
> >
> > I want to select all the ligands in my box within 4A of my protein. 
> > I looked at gmx help select and I used the command below but nothing 
> > appeared. It didn't show my default groups which correspond to the 
> > "14" for ligand and "1" for protein. Please advise me on what to do?
> > Am I missing something?
> >
> > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select 
> > `group "14" and within 0.4 of com of group "1"'
> >
> > Many thanks,
> >
> > Akash
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> > Abraham
> > Sent: 21 June 2017 11:56
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> >
> > Hi,
> >
> > You aren't getting output because you aren't actually making a 
> > selection - see "gmx help select" and its suggestions for where to 
> > look for the rest of the documentation and explained examples.
> >
> > Mark
> >
> > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash 
> > <akash.pandya...@ucl.ac.uk>
> > wrote:
> >
> > > I'm not sure if the command I entered (shown below) is correct. No 
> > > output was given. I'm unclear as to how this command will enable 
> > > me to isolate the glycine molecules within 4A of the protein molecule?
> > >
> > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos 
> > > whole_mol_com -seltype dyn_mol_com -pdbatoms all
> > >
> > > Akash
> > >
> > > -Original Message-
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
> > > Mark Abraham
> > > Sent: 16 June 2017 17:22
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> > >
> > > Hi,
> > >
> > > Gmx select will produce a selection eg of all molecules with an 
> > > atom within a cutoff of any atom in another molecule.
> > >
> > > Mark
> > >
> > > On Fri, 16 Jun 2017 18:15 Pandya, Akash 
> > > <akash.pandya...@ucl.ac.uk>
> > wrote:
> > >
> > > > Hi all,
> > > >
> > > > I have ran a simulation with a protein and multiple ligand 
> > > > molecules inserted randomly inside a box. I want to isolate 
> > > > those ligand molecules that are closest to the protein by a 
> > > > cut-off of four angstroms or so. Is there a command I could use 
> > > > to do this for me or would I have to use a molecular visualizer 
> > > > software for
> this?
> > > >
> > > > Thanks,
> > > >
> > > > Akash
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
> > > > before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit 
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-use
> > > > rs

Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

Yes it is. So that means I need a cut-off greater than right?

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 28 June 2017 11:08
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Is the radius of your protein greater than 0.4 nm?

Mark

On Wed, 28 Jun 2017 12:05 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> Hi,
>
> I want to select all the ligands in my box within 4A of my protein. I 
> looked at gmx help select and I used the command below but nothing 
> appeared. It didn't show my default groups which correspond to the 
> "14" for ligand and "1" for protein. Please advise me on what to do? 
> Am I missing something?
>
> gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group 
> "14" and within 0.4 of com of group "1"'
>
> Many thanks,
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 21 June 2017 11:56
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> Hi,
>
> You aren't getting output because you aren't actually making a 
> selection - see "gmx help select" and its suggestions for where to 
> look for the rest of the documentation and explained examples.
>
> Mark
>
> On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash 
> <akash.pandya...@ucl.ac.uk>
> wrote:
>
> > I'm not sure if the command I entered (shown below) is correct. No 
> > output was given. I'm unclear as to how this command will enable me 
> > to isolate the glycine molecules within 4A of the protein molecule?
> >
> > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos 
> > whole_mol_com -seltype dyn_mol_com -pdbatoms all
> >
> > Akash
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> > Abraham
> > Sent: 16 June 2017 17:22
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
> >
> > Hi,
> >
> > Gmx select will produce a selection eg of all molecules with an atom 
> > within a cutoff of any atom in another molecule.
> >
> > Mark
> >
> > On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk>
> wrote:
> >
> > > Hi all,
> > >
> > > I have ran a simulation with a protein and multiple ligand 
> > > molecules inserted randomly inside a box. I want to isolate those 
> > > ligand molecules that are closest to the protein by a cut-off of 
> > > four angstroms or so. Is there a command I could use to do this 
> > > for me or would I have to use a molecular visualizer software for this?
> > >
> > > Thanks,
> > >
> > > Akash
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit 
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or send a mail to gmx-users-requ...@gromacs.org.
> > >
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

Hi,

I want to select all the ligands in my box within 4A of my protein. I looked at 
gmx help select and I used the command below but nothing appeared. It didn't 
show my default groups which correspond to the "14" for ligand and "1" for 
protein. Please advise me on what to do? Am I missing something?

gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group "14" and 
within 0.4 of com of group "1"'

Many thanks, 

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 21 June 2017 11:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

You aren't getting output because you aren't actually making a selection - see 
"gmx help select" and its suggestions for where to look for the rest of the 
documentation and explained examples.

Mark

On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> I'm not sure if the command I entered (shown below) is correct. No 
> output was given. I'm unclear as to how this command will enable me to 
> isolate the glycine molecules within 4A of the protein molecule?
>
> gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos 
> whole_mol_com -seltype dyn_mol_com -pdbatoms all
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
> Abraham
> Sent: 16 June 2017 17:22
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> Hi,
>
> Gmx select will produce a selection eg of all molecules with an atom 
> within a cutoff of any atom in another molecule.
>
> Mark
>
> On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
>
> > Hi all,
> >
> > I have ran a simulation with a protein and multiple ligand molecules 
> > inserted randomly inside a box. I want to isolate those ligand 
> > molecules that are closest to the protein by a cut-off of four 
> > angstroms or so. Is there a command I could use to do this for me or 
> > would I have to use a molecular visualizer software for this?
> >
> > Thanks,
> >
> > Akash
> > --
> > Gromacs Users mailing list
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > posting!
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> > or send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] gmx distance

[Pandya, Akash]

Hi all,

I'm trying to calculate the distance between two groups using the following 
command line:


gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select `com of 
group "1" plus com of group "14"`


Group 1 is my protein and Group 14 is my ligand. There is an error message that 
shows up:

Inconsistency in user input:
Selection 'Protein' does not evaluate into an even number of positions (there
are 6617 positions)

I'm not sure how to solve this problem. Does anyone have a solution?
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

I'm not sure if the command I entered (shown below) is correct. No output was 
given. I'm unclear as to how this command will enable me to isolate the glycine 
molecules within 4A of the protein molecule?  

gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com 
-seltype dyn_mol_com -pdbatoms all

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 16 June 2017 17:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

Gmx select will produce a selection eg of all molecules with an atom within a 
cutoff of any atom in another molecule.

Mark

On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> Hi all,
>
> I have ran a simulation with a protein and multiple ligand molecules 
> inserted randomly inside a box. I want to isolate those ligand 
> molecules that are closest to the protein by a cut-off of four 
> angstroms or so. Is there a command I could use to do this for me or 
> would I have to use a molecular visualizer software for this?
>
> Thanks,
>
> Akash
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

Hi,

Is the pre-requisite for this command a separate index file for the glycine 
molecules I have?

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 16 June 2017 17:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

Gmx select will produce a selection eg of all molecules with an atom within a 
cutoff of any atom in another molecule.

Mark

On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> Hi all,
>
> I have ran a simulation with a protein and multiple ligand molecules 
> inserted randomly inside a box. I want to isolate those ligand 
> molecules that are closest to the protein by a cut-off of four 
> angstroms or so. Is there a command I could use to do this for me or 
> would I have to use a molecular visualizer software for this?
>
> Thanks,
>
> Akash
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
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[gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

Hi all,

I have ran a simulation with a protein and multiple ligand molecules inserted 
randomly inside a box. I want to isolate those ligand molecules that are 
closest to the protein by a cut-off of four angstroms or so. Is there a command 
I could use to do this for me or would I have to use a molecular visualizer 
software for this?

Thanks,

Akash
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Re: [gmx-users] Snapshots from trajectories

[Pandya, Akash]

Thank you very much. 


Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of András 
Ferenc WACHA
Sent: 12 June 2017 11:54
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Snapshots from trajectories

Dear Akash,

you might want to try gmx trjconv and give a PDB file for output (-o) and 
choose a value for -dt (-dt 1 for every 10 ns). Using -sep writes each 
frame to a different file.

I hope that helped.

Best regards,

Andras Wacha


On 06/12/2017 12:44 PM, Pandya, Akash wrote:
> Hi,
>
> Is there any way to export snapshot images from the trajectory lets say every 
> 10 ns during the course of the MD simulation?
>
>
> Akash

--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry Research Centre for Natural 
Sciences Hungarian Academy of Sciences (RCNS HAS) Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu,
CREDO SAXS instrument: http://credo.ttk.mta.hu

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[gmx-users] Snapshots from trajectories

[Pandya, Akash]

Hi,

Is there any way to export snapshot images from the trajectory lets say every 
10 ns during the course of the MD simulation?


Akash
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[gmx-users] NVT and NPT equilibration

[Pandya, Akash]

Hi all,

I want to equilibrate my system and NVT worked fine for me converging onto the 
300K set point. However, with the NPT part my average pressure is very low 
(0.22 bar) compared to the 1 bar set point. Is it necessary to do both 
equilibration steps in order to progress through to the production MD run? Or 
will NVT be suffice. I have copied my NPT mdp file to this email.

define = -DPOSRES; position restrain the protein
; Run parameters
integrator   = md; leap-frog integrator
nsteps = 25000 ; 2 * 25000 = 50 ps
dt = 0.002  ; 2 fs
; Output control
nstxout   = 100   ; save coordinates every 0.2 ps
nstvout   = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every  0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation  = yes; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter= 1   ; accuracy of LINCS
lincs_order= 4   ; also related to accuracy
; Neighborsearching
ns_type  = grid   ; search neighboring grid cells
nstlist  = 5   ; 10 fs
rlist  = 1.0; short-range neighborlist 
cutoff (in nm)
rcoulomb   = 1.0; short-range electrostatic cutoff 
(in nm)
rvdw= 1.0; short-range van der Waals 
cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range 
electrostatics
pme_order= 4   ; cubic interpolation
fourierspacing   = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more 
accurate
tau_t   = 0.1  0.1 ; time constant, in ps
ref_t= 300300; reference temperature, one for 
each group, in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman  ; Pressure coupling on in NPT
pcoupltype= isotropic  ; uniform scaling of box vectors
tau_p  = 2.0; time constant, in ps
ref_p   = 1.0; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc  = xyz; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel   = no ; Velocity generation is off

Thanks in advance,

Akash
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[gmx-users] Energy Minimisation

[Pandya, Akash]

Hi all,

I have used the steepest descent method to minimise my system. It kept saying 
certain water molecules could not be settled but it still managed to reached 
the maximum force. Then I used the Conjugate gradient method and I get this 
error message. Can someday please tell me how I would check and ultimately get 
rid of the bad contacts.

Fatal error:
The coordinates could not be constrained. Minimizer 'cg' can not handle
constraint failures, use minimizer 'steep' before using 'cg'.



Akash






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Re: [gmx-users] System Charge

[Pandya, Akash]

Hi,

Well I have to add 50mM of NaCl to my system, so I specified that on the genion 
command with the flag -conc and also entered -neutral. But it still came up 
with a charge of 9.26 so I am not sure? 

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 05 June 2017 19:30
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] System Charge

Hi,

Is that a suitable model of your simulation system? Why is it better than one 
with a different number of ions?

Mark

On Mon, 5 Jun 2017 20:22 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> Hi all,
>
> My system has still got a non-zero total charge of 9 after adding the 
> counter-ions. Do I need for it to be zero in order to run the 
> simulation or is it fine?
>
>
> Akash
>
>
>
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[gmx-users] System Charge

[Pandya, Akash]

Hi all,

My system has still got a non-zero total charge of 9 after adding the 
counter-ions. Do I need for it to be zero in order to run the simulation or is 
it fine?


Akash



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Re: [gmx-users] Minimisation

[Pandya, Akash]

One quick question what would you suggest a suitable box size is?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 4:42 PM, Pandya, Akash wrote:
> Is there a chance that as my simulation box is quite small 2 angstroms and 
> citrate is a charged anion, this could be a cause of my system blowing up?
>

I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.

-Justin

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Justin Lemkul
> Sent: 22 May 2017 13:26
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 7:25 AM, Pandya, Akash wrote:
>> What could be wrong with the topology could you please elaborate? I added 
>> glycine and citrate molecules  to the simulation box randomly. Could it be 
>> the fact I added topology for glycine and citrate in the wrong way?
>>
>> This is how my topol.top file looks:
>>
>> ; Include Citrate Topology
>> #include "Citrate.itp"
>> #ifdef POSRES
>> #include "Citrate_posre.itp"
>> #endif
>>
>> ; Include GLY Topology
>> #include "GLY.itp"
>> #ifdef POSRES
>> #include "GLY_posre.itp"
>> #endif
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Protein_chain_H 3
>>
>
> A series of #include statements is not a useful diagnostic.  You should start 
> by inspecting your coordinates, particularly whatever atom 6640 is, and its 
> surroundings.  There may simply be a bad clash there that can be resolved 
> easily.  Otherwise, follow 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   Glycine should come from the force field itself and likely is not 
> topologically problematic, but if you constructed your own citrate 
> parameters, you should check their correctness, as well.
>
> -Justin
>
>> Akash
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
>> Of Justin Lemkul
>> Sent: 22 May 2017 12:13
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Minimisation
>>
>>
>>
>> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>>> Hi all,
>>>
>>>
>>> During Minimisation I get the following output that the simulation ended 
>>> prematurely.
>>>
>>>
>>>
>>> Steepest Descents:
>>>Tolerance (Fmax)   =  1.0e+03
>>>Number of steps=   50
>>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>>
>>> Energy minimization has stopped, but the forces have not converged 
>>> to the requested precision Fmax < 1000 (which may not be possible for your 
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size 
>>> was too small, or there was no change in the energy since last step.
>>> Either way, we regard the minimization as converged to within the 
>>> available machine precision, given your starting configuration and EM 
>>> parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is 
>>> often not needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn off 
>>> constraints altogether (set constraints = none in mdp file)
>>>
>>> How do I increase my constraint accuracy? Which file do I have to change?
>>>
>>
>> That's not your problem.  You have infinite force, which means you have some 
>> catastrophic problem with either your coordinates or topology.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences School of Pharmacy Health 
>> Sciences Facility II, Room 629 University of Maryland, Baltimor

Re: [gmx-users] Minimisation

[Pandya, Akash]

Sorry I meant 20 A. But I'll look into expanding the box size and see if it 
works. Thanks for your help.

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 4:42 PM, Pandya, Akash wrote:
> Is there a chance that as my simulation box is quite small 2 angstroms and 
> citrate is a charged anion, this could be a cause of my system blowing up?
>

I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.

-Justin

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Justin Lemkul
> Sent: 22 May 2017 13:26
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 7:25 AM, Pandya, Akash wrote:
>> What could be wrong with the topology could you please elaborate? I added 
>> glycine and citrate molecules  to the simulation box randomly. Could it be 
>> the fact I added topology for glycine and citrate in the wrong way?
>>
>> This is how my topol.top file looks:
>>
>> ; Include Citrate Topology
>> #include "Citrate.itp"
>> #ifdef POSRES
>> #include "Citrate_posre.itp"
>> #endif
>>
>> ; Include GLY Topology
>> #include "GLY.itp"
>> #ifdef POSRES
>> #include "GLY_posre.itp"
>> #endif
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Protein_chain_H 3
>>
>
> A series of #include statements is not a useful diagnostic.  You should start 
> by inspecting your coordinates, particularly whatever atom 6640 is, and its 
> surroundings.  There may simply be a bad clash there that can be resolved 
> easily.  Otherwise, follow 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   Glycine should come from the force field itself and likely is not 
> topologically problematic, but if you constructed your own citrate 
> parameters, you should check their correctness, as well.
>
> -Justin
>
>> Akash
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
>> Of Justin Lemkul
>> Sent: 22 May 2017 12:13
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Minimisation
>>
>>
>>
>> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>>> Hi all,
>>>
>>>
>>> During Minimisation I get the following output that the simulation ended 
>>> prematurely.
>>>
>>>
>>>
>>> Steepest Descents:
>>>Tolerance (Fmax)   =  1.0e+03
>>>Number of steps=   50
>>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>>
>>> Energy minimization has stopped, but the forces have not converged 
>>> to the requested precision Fmax < 1000 (which may not be possible for your 
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size 
>>> was too small, or there was no change in the energy since last step.
>>> Either way, we regard the minimization as converged to within the 
>>> available machine precision, given your starting configuration and EM 
>>> parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is 
>>> often not needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn off 
>>> constraints altogether (set constraints = none in mdp file)
>>>
>>> How do I increase my constraint accuracy? Which file do I have to change?
>>>
>>
>> That's not your problem.  You have infinite force, which means you have some 
>> catastrophic problem with either your coordinates or topology.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences School of Pharmacy Health 
>> Sciences Facility I

Re: [gmx-users] Minimisation

[Pandya, Akash]

Is there a chance that as my simulation box is quite small 2 angstroms and 
citrate is a charged anion, this could be a cause of my system blowing up?   

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 22 May 2017 13:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 7:25 AM, Pandya, Akash wrote:
> What could be wrong with the topology could you please elaborate? I added 
> glycine and citrate molecules  to the simulation box randomly. Could it be 
> the fact I added topology for glycine and citrate in the wrong way?
>
> This is how my topol.top file looks:
>
> ; Include Citrate Topology
> #include "Citrate.itp"
> #ifdef POSRES
> #include "Citrate_posre.itp"
> #endif
>
> ; Include GLY Topology
> #include "GLY.itp"
> #ifdef POSRES
> #include "GLY_posre.itp"
> #endif
>
> [ moleculetype ]
> ; Namenrexcl
> Protein_chain_H 3
>

A series of #include statements is not a useful diagnostic.  You should start 
by inspecting your coordinates, particularly whatever atom 6640 is, and its 
surroundings.  There may simply be a bad clash there that can be resolved 
easily.  Otherwise, follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  Glycine should come from the force field itself and likely is not 
topologically problematic, but if you constructed your own citrate parameters, 
you should check their correctness, as well.

-Justin

> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
> Of Justin Lemkul
> Sent: 22 May 2017 12:13
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>> Hi all,
>>
>>
>> During Minimisation I get the following output that the simulation ended 
>> prematurely.
>>
>>
>>
>> Steepest Descents:
>>Tolerance (Fmax)   =  1.0e+03
>>Number of steps=   50
>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>> 6640
>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>> 6640
>>
>> Energy minimization has stopped, but the forces have not converged to 
>> the requested precision Fmax < 1000 (which may not be possible for your 
>> system).
>> It stopped because the algorithm tried to make a new step whose size 
>> was too small, or there was no change in the energy since last step.
>> Either way, we regard the minimization as converged to within the 
>> available machine precision, given your starting configuration and EM 
>> parameters.
>>
>> Double precision normally gives you higher accuracy, but this is 
>> often not needed for preparing to run molecular dynamics.
>> You might need to increase your constraint accuracy, or turn off 
>> constraints altogether (set constraints = none in mdp file)
>>
>> How do I increase my constraint accuracy? Which file do I have to change?
>>
>
> That's not your problem.  You have infinite force, which means you have some 
> catastrophic problem with either your coordinates or topology.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441 
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
--
Gro

Re: [gmx-users] Minimisation

[Pandya, Akash]

What could be wrong with the topology could you please elaborate? I added 
glycine and citrate molecules  to the simulation box randomly. Could it be the 
fact I added topology for glycine and citrate in the wrong way?

This is how my topol.top file looks:

; Include Citrate Topology
#include "Citrate.itp"
#ifdef POSRES
#include "Citrate_posre.itp"
#endif

; Include GLY Topology
#include "GLY.itp"
#ifdef POSRES
#include "GLY_posre.itp"
#endif

[ moleculetype ]
; Namenrexcl
Protein_chain_H 3

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 22 May 2017 12:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 6:47 AM, Pandya, Akash wrote:
> Hi all,
>
>
> During Minimisation I get the following output that the simulation ended 
> prematurely.
>
>
>
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+03
>Number of steps=   50
> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
>
> Energy minimization has stopped, but the forces have not converged to 
> the requested precision Fmax < 1000 (which may not be possible for your 
> system).
> It stopped because the algorithm tried to make a new step whose size 
> was too small, or there was no change in the energy since last step. 
> Either way, we regard the minimization as converged to within the 
> available machine precision, given your starting configuration and EM 
> parameters.
>
> Double precision normally gives you higher accuracy, but this is often 
> not needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn off 
> constraints altogether (set constraints = none in mdp file)
>
> How do I increase my constraint accuracy? Which file do I have to change?
>

That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Minimisation

[Pandya, Akash]

Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

How do I increase my constraint accuracy? Which file do I have to change?

Best wishes,

Akash
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Re: [gmx-users] Error with moleculetype

[Pandya, Akash]

Tried to put it at the end but it still came up with the same error. 

Justin, I don't understand what you mean?

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 19 May 2017 22:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error with moleculetype



On 5/19/17 5:33 PM, Mark Abraham wrote:
> Hi,
>
> Ok. Maybe it needs to be last in the molecules?
>

Or perhaps the error points to a malformed line ending that causes genion to 
choke when updating the topology.

-Justin

> Mark
>
> On Fri, 19 May 2017 23:19 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
>
>> It was the genion command. Here is the message.
>>
>> Fatal error:
>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>> file 'topol.top'
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
>> Abraham
>> Sent: 19 May 2017 21:26
>> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Error with moleculetype
>>
>> Hi,
>>
>> I don't think grompp can issue that message. What was the message you 
>> copied and pasted from your terminal?
>>
>> Mark
>>
>> On Fri, 19 May 2017 18:49 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> I have received an error message shown below.
>>>
>>> Fatal error:
>>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>>> file 'topol.top'
>>>
>>> For more information and tips for troubleshooting, please check the 
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>>
>>> I don't understand what's wrong with my topol.top file. I have 
>>> included the following before the [ molecules ] section.
>>>
>>> [ moleculetype ]
>>> ; Name
>>> SOL 1
>>>
>>> My [ molecules ] section looks like this:
>>>
>>> [ molecules ]
>>> ; Compound#mols
>>> Protein_chain_H 1
>>> SOL 73337
>>> Citrate29
>>> GLY   984
>>>
>>>
>>> I have read the documentation and still don't understand. Please can 
>>> you advise me on what to do?
>>>
>>> Many thanks,
>>> Akash
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
>>> or send a mail to gmx-users-requ...@gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Error with moleculetype

[Pandya, Akash]

It was the genion command. Here is the message.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 19 May 2017 21:26
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Error with moleculetype

Hi,

I don't think grompp can issue that message. What was the message you copied 
and pasted from your terminal?

Mark

On Fri, 19 May 2017 18:49 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote:

> Hi all,
>
> I have received an error message shown below.
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of 
> file 'topol.top'
>
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
>
> I don't understand what's wrong with my topol.top file. I have 
> included the following before the [ molecules ] section.
>
> [ moleculetype ]
> ; Name
> SOL 1
>
> My [ molecules ] section looks like this:
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_H 1
> SOL 73337
> Citrate29
> GLY   984
>
>
> I have read the documentation and still don't understand. Please can 
> you advise me on what to do?
>
> Many thanks,
> Akash
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Error with moleculetype

[Pandya, Akash]

Hi all,

I have received an error message shown below.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I don't understand what's wrong with my topol.top file. I have included the 
following before the [ molecules ] section.

[ moleculetype ]
; Name
SOL 1

My [ molecules ] section looks like this:

[ molecules ]
; Compound#mols
Protein_chain_H 1
SOL 73337
Citrate29
GLY   984


I have read the documentation and still don't understand. Please can you advise 
me on what to do?

Many thanks,
Akash

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Re: [gmx-users] Error message

[Pandya, Akash]

Hi,

Thank you for your response. A new issue has arisen. The itp file was generated 
from SWISS PARAM. I don't understand why it can't recognise the NRP atomtype 
for Nitrogen.

ERROR 1 [file GLY.itp, line 17]:
  Atomtype NRP not found

Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 18 May 2017 18:03
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error message

Hi,

A molecule itp does not stand in isolation.

>From that link "If the directive in question is atomtypes (which is the most 
>common source of this error) or any other bonded or nonbonded [*types] 
>directive, typically the user is adding some non-standard species (ligand, 
>solvent, etc) that introduces new atom types or parameters into the system.
As indicated above, these new types and parameters must appear before any 
[moleculetype] directive. The force field has to be fully constructed before 
any molecules can be defined."

Probably you're including that .itp after some other [moleculetype].
Declare all the atom types before any moleculetypes, like chapter 5 of the 
reference manual documents.

Mark

On Thu, May 18, 2017 at 6:47 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Sorry for replying on the wrong thread. I've read the errors 
> documentation. The atomtypes directive does appear before any molecule 
> types directive in my itp file. I tried changing the order it still 
> comes up as an error
>
> [ atomtypes ]
> ; name atomnum  masscharge  ptype sigma epsilon
> CR 6   12.0110   0.0A  0.3875410.230120
> CO2M   6   12.0110   0.0A  0.3563590.292880
> HCMM   11.0079   0.0A  0.2351970.092048
> HNRP   11.0079   0.0A  0.0400010.192464
> NRP7   14.0067   0.0A  0.3296320.836800
> O2CM   8   15.9994   0.0A  0.3029050.502080
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
> Lemkul
> Sent: 18 May 2017 17:00
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error message
>
>
>
> On 5/18/17 11:57 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I've been trying to figure out the error message below but I'm not
> getting anywhere. I have attached my relevant itp file. Please could 
> someone tell me what is wrong with my itp file?
> >
>
> Googling the error usually turns something up...
>
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directiv
> e_xxx
>
> For future reference, the list does not accept attachments.
>
> -Justin
>
> >
> > Fatal error:
> > Syntax error - File GLY.itp, line 7
> > Last line read:
> > '[ atomtypes ] '
> > Invalid order for directive atomtypes
> >
> >
> > Best regards,
> >
> > Akash
> >
> >
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441 
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] Error message

[Pandya, Akash]

Sorry for replying on the wrong thread. I've read the errors documentation. The 
atomtypes directive does appear before any molecule types directive in my itp 
file. I tried changing the order it still comes up as an error

[ atomtypes ]
; name atomnum  masscharge  ptype sigma epsilon
CR 6   12.0110   0.0A  0.3875410.230120
CO2M   6   12.0110   0.0A  0.3563590.292880
HCMM   11.0079   0.0A  0.2351970.092048
HNRP   11.0079   0.0A  0.0400010.192464
NRP7   14.0067   0.0A  0.3296320.836800
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 17:00
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error message



On 5/18/17 11:57 AM, Pandya, Akash wrote:
> Hi all,
>
> I've been trying to figure out the error message below but I'm not getting 
> anywhere. I have attached my relevant itp file. Please could someone tell me 
> what is wrong with my itp file?
>

Googling the error usually turns something up...

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

For future reference, the list does not accept attachments.

-Justin

>
> Fatal error:
> Syntax error - File GLY.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
>
>
> Best regards,
>
> Akash
>
>
>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Pandya, Akash]

I've read the errors documentation. The atomtypes directive does appear before 
any molecule types directive in my itp file. I tried changing the order it 
still comes up as an error

[ atomtypes ] 
; name atomnum  masscharge  ptype sigma epsilon 
CR 6   12.0110   0.0A  0.3875410.230120  
CO2M   6   12.0110   0.0A  0.3563590.292880   
HCMM   11.0079   0.0A  0.2351970.092048  
HNRP   11.0079   0.0A  0.0400010.192464  
NRP7   14.0067   0.0A  0.3296320.836800  
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 16:33
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Can you please tell me the exact command? Re: Restart 
a stopped simulation after a power failure? : Not working in Gromacs 5.1.4



On 5/18/17 11:30 AM, Adarsh V. K. wrote:
> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue 
> for couple month time. Would you please advise me how to use  " 
> -deffnm " flag in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation 
> and append?, If no could you please type the exact command I 
> should use to solve the issue.
>

The -deffnm command sets the default file prefix for all output files.  So if 
you issue:

gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)

gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin

> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C ) Kerala state, 
> India
>
> --
>  On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> 
> wrote:
>
>> Hi,
>>
>> Some of your commands and outputs are inconsistent. You can't get 
>> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if 
>> you don't use deffnm. But if you change that when trying to do your 
>> continuation, mdrun won't know how to append because you haven't told 
>> it that the old name. Be consistent. Your whole trajectory is present 
>> in all your output files, but you're going to have to concatenate 
>> them yourself, e.g. with gmx trjcat since you didn't tell mdrun a 
>> consistent name for the files.
>>
>> GROMACS 2016 likely refuses to do your continuation, precisely so 
>> that you are prompted to say what you actually want, rather than 
>> mdrun trying to be clever and getting it wrong.
>>
>> Mark
>>
>> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
>> 
>> wrote:
>>
>>> Dear gmx users,
>>>
>>> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart 
>>> a stopped simulation after a power failure? (used 8 processor cores 
>>> + Graphics card GTX 780Ti).
>>>
>>> I have attached the log file along with this mail.
>>>
>>> It appeared that no details appended after restarting simulation 
>>> (after power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 
>>> 16.04 shows that the simulation successfully restarted from 3.5 ns 
>>> (used 8 processor cores + Graphics card GTX 780Ti) and completed the 
>>> entire 8 ns simulation...!!. Frames...350 -> 3500 ps (not appended 
>>> the log file after the restart from 3500ps to 8000ps).
>>>
>>> I used the command (gromacs 5.1.4),
>>>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>>
>>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
>>>
>>> 
>>> 
>>> md_0_1.log : (final)
>>> -
>>> Step   Time Lambda
>>> 1765000 3530.00.0
>>>
>>>Energies (kJ/mol)
>>>G96AngleProper Dih.  Improper Dih.  LJ-14
>>> Coulomb-14
>>> 6.73096e+033.13198e+032.15931e+031.31375e+03
>>> 4.51549e+04
>>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
>>> -2.29382e+06
>>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>>> (bar)
>>> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
>>> 2.10104e+01
>>>Constr. rmsd
>>> 2.37431e-05
>>> 
>>> -
>>> md.log (final)
>>> --
>>> Step   Time Lambda
>>> 400 8000.00.0
>>>
>>> Writing checkpoint, step 

[gmx-users] Error message

[Pandya, Akash]

Hi all,

I've been trying to figure out the error message below but I'm not getting 
anywhere. I have attached my relevant itp file. Please could someone tell me 
what is wrong with my itp file?


Fatal error:
Syntax error - File GLY.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes


Best regards,

Akash
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[gmx-users] Calculating number of molecules to add in simulation box

[Pandya, Akash]

Hi all,

I'm trying to calculate the number of Glycine molecules to add into the 
simulation box. The molar concentration of glycine I'm using is 0.67M. My 
simulation box size is 2nm and the box volume is 2440.78nm^3. How would I 
calculate the number of glycine molecules to fulfil this molar concentration?


Best wishes,

Akash

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[gmx-users] Calculating the number of ligand molecules needed inside the simulation box

[Pandya, Akash]

Hi all,

I'm trying to add ligands into a simulation box without being a part of a 
complex. I'm not sure how to calculate the number of ligand molecules I need to 
achieve my specific concentration? Do I go according to the box volume? Could 
anyone tell me how I should go about this?


Many thanks,

Akash
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Re: [gmx-users] Adding buffer to simulation box

[Pandya, Akash]

I'm using the OPLS ff but I can't seem to find a tool in which I can generate 
topology for this force field. I looked up the ones recommended on GROMACS but 
had no luck. I also have SWISSParam but that is for CHARMM.

Akash  

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 02 May 2017 16:27
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Adding buffer to simulation box

Hi,

Everything that goes into your simulation cell has to have a topology file, so 
you'll need to develop one for citrate anion. And then do the simple arithmetic 
to work out how many of each species you need in your cell to be a model of 
your conditions of interest.

Mark

On Tue, May 2, 2017 at 4:53 PM Pandya, Akash <akash.pandya...@ucl.ac.uk>
wrote:

> Hi all,
>
>
>
> I want to run an MD simulation in presence of 20mM Sodium Citrate 
> buffer at pH4.5 . How would I go about adding this buffer to the 
> simulation box? I have tried adding it in the same way as counter-ions 
> but it did not work. I am aware of the gmx insert molecules command 
> but I'm not sure whether I need a buffer topology file for this?
>
>
>
> Akash
>
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[gmx-users] Adding buffer to simulation box

[Pandya, Akash]

Hi all,



I want to run an MD simulation in presence of 20mM Sodium Citrate buffer at 
pH4.5 . How would I go about adding this buffer to the simulation box? I have 
tried adding it in the same way as counter-ions but it did not work. I am aware 
of the gmx insert molecules command but I'm not sure whether I need a buffer 
topology file for this?



Akash

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