Re: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

[Jianguo Li]

Why not use CHARMM36 FF? It is available in gromacs user contribution website.

If I remember correctly, charmm27 cannot yield correct area/lipid, you need to 
apply surface tension.

Cheeers,
Jianguo



From: Jackson Chief 
To: gmx-users@gromacs.org
Sent: Monday, 5 September 2011 21:20:48
Subject: [gmx-users] Error when performing grompp on lipid bilayer modeled with 
CHARMM27

I want to make a model of a GPCR inserted into lipid bilayer.  I obtained the 
structure file for a solvated POPC bilayer from the CHARMM-GUI site.  I used 
CHARMM27 force field to model the bilayer and pdb2gmx had no problem generating 
the *.gro, *.top, and posre.itp files.  When I perform grompp I receive the 
following warning and error;

"WARNING 1 [file ffnonbonded.itp, line 130]:
  Overriding atomtype HOL"

"ERROR 1 [file bilayer.top, line 271489]:
  No default U-B types"

I though that the issue with creating Urey-Bradley interactions using pdb2gmx 
had been corrected in Gromacs-4.5.4.  Please give me some advice on how to 
proceed further.

Thank you,
Jackson Chief Elk-- 
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[gmx-users] atom type OXT

[Sweta Iyer]

Hi all,

I have been trying to pdbgmx my protein to obtain the gro and top files as 
follows:

pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter  -ignh

However, I get an error message that states:

Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
while sorting atoms

I figure from previous threads that many ppl have been facing the similar 
issue. I also happened to go through the discussion in the bugs page.
This is how my pdb file looks like. Where would i have to re name my oxygen 
atoms in order to fix this?

ATOM  1  N   LEU X   1  36.020  45.310   8.310  1 1 1.63 
-0.15
ATOM  2  CA  LEU X   1  36.400  43.890   8.240  2 1 2.03  
0.10
ATOM  3  CB  LEU X   1  37.910  43.930   7.990  6 1 1.99  
0.00
ATOM  4  CG  LEU X   1  38.320  44.530   6.640 16 1 2.03  
0.00
ATOM  5  CD1 LEU X   1  39.830  44.320   6.680 17 1 1.94  
0.00
ATOM  6  CD2 LEU X   1  37.710  43.760   5.470 17 1 1.94  
0.00
ATOM  7  C  LEU X   1  35.910  43.180   9.510  3 1 1.67 
 0.60
ATOM  8  O   LEU X   1  36.680  43.050  10.460  4 1 1.38 
-0.55
ATOM  9  N   GLY X   2  34.710  42.620   9.390  1 1 1.63 
-0.15
ATOM 10  CA  GLY X   2  33.850  42.050  10.440  5 1 1.99  
0.10
ATOM 11  C   GLY X   2  34.300  40.610  10.700  3 1 1.67  
0.60
ATOM 12  O   GLY X   2  33.470  39.700  10.770  4 1 1.38 
-0.55
ATOM 13  N   ASN X   3  35.500  40.620  11.270  1 1 1.63 
-0.15
ATOM 14  CA  ASN X   3  36.180  39.350  11.510  2 1 2.03  
0.10
ATOM 15  CB  ASN X   3  37.610  39.430  10.970  6 1 1.99  
0.00
ATOM 16  CG  ASN X   3  37.560  39.470   9.440 11 1 1.67  
0.55
ATOM 17  OD1 ASN X   3  36.740  38.900   8.720 11 1 1.38 
-0.55
ATOM 18  ND2 ASN X   3  38.500  40.150   8.800 11 1 1.63  
0.00
ATOM 19  C   ASN X   3  36.140  38.770  12.930  3 1 1.67  
0.60
ATOM 20  O   ASN X   3  37.200  38.510  13.500  4 1 1.38 
-0.55
ATOM 21  N   GLY X   4  34.910  38.860  13.410  1 1 1.63 
-0.15
ATOM 22  CA  GLY X   4  34.410  38.420  14.720  5 1 1.99  
0.10
ATOM 23  C   GLY X   4  34.630  36.920  14.890  3 1 1.67  
0.60
ATOM 24  O   GLY X   4  34.060  36.200  14.070  4 1 1.38 
-0.55
ATOM 25  N   PRO X   5  35.630  36.460  15.640  1 0 1.63 
-0.25
ATOM 26  CA  PRO X   5  36.100  35.070  15.570  2 1 2.03  
0.10
ATOM 27  CB  PRO X   5  37.580  35.090  15.950  6 1 1.99  
0.00
ATOM 28  CG  PRO X   5  37.700  36.360  16.780  6 1 1.99  
0.00
ATOM 29  CD  PRO X   5  36.510  37.270  16.500  6 1 1.99  
0.10
ATOM 30  C   PRO X   5  35.290  34.130  16.470  3 0 1.67  
0.60
ATOM 31  O   PRO X   5  35.300  34.320  17.690  4 0 1.38 
-0.55
ATOM 32  N   ILE X   6  34.630  33.150  15.870  1 1 1.63 
-0.15
ATOM 33  CA  ILE X   6  33.650  32.240  16.500  2 1 2.03  
0.10
ATOM 34  CB  ILE X   6  33.090  31.180  15.550  6 1 2.03  
0.00
ATOM 35  CG1 ILE X   6  32.320  31.810  14.400 16 1 1.99  
0.00
ATOM 36  CG2 ILE X   6  32.170  30.220  16.310 17 1 1.94  
0.00
ATOM 37  CD  ILE X   6  31.910  30.940  13.210 17 1 1.94  
0.00
ATOM 38  C   ILE X   6  34.280  31.620  17.750  3 0 1.67  
0.60
ATOM 39  O   ILE X   6  33.860  31.920  18.870  4 0 1.38 
-0.55
ATOM 40  N   LEU X   7  35.460  31.050  17.520  1 0 1.63 
-0.15
ATOM 41  CA  LEU X   7  36.260  30.330  18.520  2 0 2.03  
0.10
ATOM 42  CB  LEU X   7  37.480  29.600  17.970  6 1 1.99  
0.00
ATOM 43  CG  LEU X   7  37.050  28.470  17.030 16 1 2.03  
0.00
ATOM 44  CD1 LEU X   7  38.310  28.200  16.220 17 1 1.94  
0.00
ATOM 45  CD2 LEU X   7  36.700  27.200  17.810 17 1 1.94  
0.00
ATOM 46  C   LEU X   7  36.640  31.270  19.670  3 0 1.67  
0.60
ATOM 47  O   LEU X   7  36.630  30.820  20.820  4 0 1.38 
-0.55
ATOM 48  N   ASN X   8  36.880  32.550  19.390  1 0 1.63 
-0.15
ATOM 49  CA  ASN X   8  37.240  33.460  20.490  2 0 2.03  
0.10
ATOM 50  CB  ASN X   8  38.030  34.660  19.970  6 1 1.99  
0.00
ATOM 51  CG  ASN X   8  39.510  34.340  19.760 11 1 1.67  
0.55
ATOM 52  OD1 ASN X   8  40.030  33.230  19.760 11 1 1.38 
-0.55
ATOM 53  ND2 ASN X   8  40.270  35.420  19.930 11 1 1.63  
0.

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

[Mark Abraham]

On 6/09/2011 1:44 AM, J. Nathan Scott wrote:



On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham > wrote:


On 6/09/2011 1:22 AM, J. Nathan Scott wrote:



On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 5/09/2011 3:30 AM, J. Nathan Scott wrote:

Hello fellow GROMACS users,

I am in the process of constructing a new residue in the
OPLS-AA force field for the mCherry chromophore. However,
I am having some difficulty in adding three CH3
hydrogens. In the 2H5Q PDB structure the chromophore
residue, CH6, has CE1 and CE2 ring carbons defined, but
also an extended chain carbon named CE. The problem is
that my hdb rules were assigning HE1 and HE2 to the ring
carbon hydrogens (1   1   HE1 CE1 CD1
CZ for example), and HE1, HE2, and HE3 to the CE carbon

hydrogens (3   4   HE CE SD  CG1).
Since these hydrogens are of different types, I need to
have them named distinctly in my RTP file and need for
Gromacs to understand them as different types. I changed
the CH6 residue's CE atom to CE3 in the PDB file and the
relevant RTP entries accordingly (see below). I also
changed the hdb entry for the new CE3 atom (also below).

Relevant RTP lines:
  CE3opls_209  0.0 10
 HE31opls_140  0.0 11
 HE32opls_140  0.0 12
 HE33opls_140  0.0 13
  CE1opls_145  0.0 32
  HE1opls_146  0.0 33
  CE2opls_145  0.0 34
  HE2opls_146  0.0 35
 [bonds]
  CE3  HE31
  CE3  HE32
  CE3  HE33
  CE1   HE1
  CE2   HE2

Relevant HDB lines:
3   4   HE3 CE3 SD  CG1
1   1   HE1 CE1 CD1 CZ
1   1   HE2 CE2 CD2 CZ

I thought this would cover everything, but I am receiving
the following sort of error from pdb2gmx for each of the
the three CE3 hydrogens(pdb2gmx -f 2H5Q.pdb -o
2H5Q_processed.gro -water tip3):

"WARNING: atom HE31 is missing in residue CH6 66 in the
pdb file
You might need to add atom HE31 to the hydrogen
database of building block CH6
in the file aminoacids.hdb (see the manual)"

I've looked at other examples in the aminoacids.hdb file
and cannot figure out what I am missing here, it seems
like my hdb rule should be adding 3 type 4 hydrogens
named HE31, HE32, and HE33. I am assuming that the other
hdb rules are OK, since they seemed to work fine before,
as indicated by examining the gro file. I would sincerely
appreciate any help you can offer. Thank you!


I can't see a reason why that wouldn't work. However, there's
no need for you to preserve the PDB atom name for CE.
Reducing the potential for some atom-naming screw-up such as
this is a good reason to change it (in both your coordinate
file and .rtp entry). It will probably just work, or at the
very least simplify further trouble-shooting.

Mark


Hello Mark, thank you for your help, but I took your very
reasonable advice and am still receiving the exact same sort of
error. I changed the PDB file atom name to CQ, which of course
makes it unique within that residue (and indeed in the whole PDB
file). I updated my .rtp entries and the .hdb rules accordingly,
and yet I still receive the exact same sort of error. It seems as
if something is wrong with my hdb syntax, but having looked at
numerous other examples in the hdb file and online I am at a loss
as to what the problem might be. For what it's worth, if I use
the -missing switch when I run pdb2gmx, the other CH6 hydrogen
atoms appear to be added correctly in the resulting gro file,
with the names exactly as I expected from the hdb naming rules.


My input:
pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3

Error received:
"WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database
of building block CH6
 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database
of building block CH6
 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ3 is missing in residue CH6 66 in t

Re: [gmx-users] Counting number of non-bonded interactions ?

[Mark Abraham]

On 6/09/2011 3:40 AM, Chih-Ying Lin wrote:



Hi
Is there any function to count number of non-bonded interactions with 
Gromacs ?




Before or after cut-offs? Interaction types or actual interactions?

Mark
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Re: [gmx-users] REMD Error

[Jose Tusell]

Hi Mark,

I just posted a bug on redmine for the remd problem that I encountered.  I
was as thorough as possible about how to recreate the bug, but if I forgot
some crucial piece of information let me know and I will get it to you as
soon as possible.  Thanks for your time.

Jose Tusell

On Sat, Sep 3, 2011 at 9:41 AM, Jose Tusell  wrote:

> Mark,
>
> I've check the *.tpr files for inconsistencies in steps and init_step and
> found that they are both the same.  I'll file a bug report in redmine and
> I'll attach all the necessary information about the initial setup.
>
> Jose R Tusell
>
>
> On Fri, Sep 2, 2011 at 11:55 PM, Mark Abraham wrote:
>
>> On 3/09/2011 3:08 PM, Jose Tusell wrote:
>>
>>> I know this error has been reported before and Mark Abraham suggested to
>>> file a bug report on redmine.  While starting regular NPT remd on my system
>>> I run into the following problem:
>>>
>>> init_step+nsteps is not equal for all subsystems
>>>  subsystem 0: 2500
>>>  subsystem 1: 0
>>>  subsystem 2: 2500
>>>  subsystem 3: 0
>>>  subsystem 4: 2500
>>>  subsystem 5: 0
>>>  subsystem 6: 2500
>>>  subsystem 7: 0
>>>  subsystem 8: 2500
>>>  subsystem 9: 0
>>>  subsystem 10: 2500
>>>  subsystem 11: 0
>>>  subsystem 12: 2500
>>>
>>> --**-
>>> Program mdrun_mpi_d, VERSION 4.5.4
>>> Source code file: main.c, line: 249
>>>
>>> Fatal error:
>>> The 64 subsystems are not compatible
>>>
>>> gmxdump gives the same nsteps and init_step.  Let me know what you'd need
>>> to file a bug on redmine.
>>>
>>
>> A description of how to reproduce the problem, GROMACS version and input
>> files to re-create the problem in a short run. Assuming you're not
>> deliberately providing mismatching .tpr files, the question becomes how
>> init_step + nsteps becomes different for the different .tpr files. That
>> seems to be during grompp, since gmxdump agrees on the contents of the .tpr
>> files.
>>
>> Mark
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>>
>
>
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RE: [gmx-users] Deuterium order parametr

[Parthasarathi, Ramya]

Sorry did not send the email.. was sent by mistake due to some error in the 
mail box. I apologise..
Ramya

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Justin A. Lemkul
Sent: Monday, September 05, 2011 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Deuterium order parametr



Parthasarathi, Ramya wrote:
> Hi,
> 
>  
> 
> I am trying to write a code for Deuterium order parameter of DOPC lipid. 
> I went through the code in gmx_order.c, I did the following,
> 
>  
> 
> 1.   I took the carbons in the chain, and found its neighbors.
> 
> 2.   Took the bilayer normal and found the angle between the bilayer 
> normal and the -CH molecular axis.
> 
> 3.   Took care of the periodic boundary conditions since I use NPT 
> ensemble.
> 
>  
> 
> But the code in gmx_order.c in GROMACS tries to do a lot of things other 
> than this, as I don't know C or C++ language that it is using, I don't 
> know what else I am supposed to include.
> 
>  
> 
> Can someone please help me?
> 
>  

My last reply should have given you some indication that your code is wrong, 
but 
the purpose of this list is not to critique your coding or teach you how to 
write programs.  You've not given any real specifics on what you're doing aside 
from a basic outline that suggests the overall workflow is correct.  The end 
result, however, is not, and that's all anyone can tell.  You'd be best served 
trying to learn how g_order works, or otherwise find suitable code in a 
language 
with which you are familiar.

-Justin

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Deuterium order parametr

[Justin A. Lemkul]

Parthasarathi, Ramya wrote:

Hi,

 

I am trying to write a code for Deuterium order parameter of DOPC lipid. 
I went through the code in gmx_order.c, I did the following,


 


1.   I took the carbons in the chain, and found its neighbors.

2.   Took the bilayer normal and found the angle between the bilayer 
normal and the –CH molecular axis.


3.   Took care of the periodic boundary conditions since I use NPT 
ensemble.


 

But the code in gmx_order.c in GROMACS tries to do a lot of things other 
than this, as I don’t know C or C++ language that it is using, I don’t 
know what else I am supposed to include.


 


Can someone please help me?

 


My last reply should have given you some indication that your code is wrong, but 
the purpose of this list is not to critique your coding or teach you how to 
write programs.  You've not given any real specifics on what you're doing aside 
from a basic outline that suggests the overall workflow is correct.  The end 
result, however, is not, and that's all anyone can tell.  You'd be best served 
trying to learn how g_order works, or otherwise find suitable code in a language 
with which you are familiar.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Deuterium order parametr

[Parthasarathi, Ramya]

Hi,

I am trying to write a code for Deuterium order parameter of DOPC lipid. I went 
through the code in gmx_order.c, I did the following,

1.   I took the carbons in the chain, and found its neighbors.
2.   Took the bilayer normal and found the angle between the bilayer normal 
and the -CH molecular axis.
3.   Took care of the periodic boundary conditions since I use NPT ensemble.

But the code in gmx_order.c in GROMACS tries to do a lot of things other than 
this, as I don't know C or C++ language that it is using, I don't know what 
else I am supposed to include.

Can someone please help me?

Ramya

-- 
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[gmx-users] Counting number of non-bonded interactions ?

[Chih-Ying Lin]

Hi
Is there any function to count number of non-bonded interactions with
Gromacs ?


Thank you
Lin
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Re: [gmx-users] problem in topology with AMBER99SB

[Justin A. Lemkul]

Anna Marabotti wrote:

Dear gmx-users,
I'm trying to create the topology for a ligand using Amber99SB force 
field, but I'm experimenting several problems. Here what I did:

 - I recovered the .mol2 file of my ligand (comp1.mol2)
- I checked and added H with Amber tool reduce: reduce comp1.mol2 > 
comp1-H.mol2
- I added charges using antechamber: antechamber -i comp1-H.mol2 -fi 
mol2 -o comp1-H_C.mol2 -fo mol2 -c bcc -s2
- I created the frcmod parameter file: parmcheck -i comp1-H_C.mol2 -f 
mol2 -o comp1-H_C.frcmod 
- then I used: xleap -s -f /opt/amber11/dat/leap/cmd/leaprc.ff99SB

source leaprc.gaff
lig = loadmol2 comp1-H_C.mol2
check lig
loadamberparams comp1-H_C.frcmod
saveamberparm lig comp1.prmtop comp1.inpcrd
- I created the .top file with amb2gmx.pl: amb2gmx.pl --prmtop 
comp1.prmtop --crd comp1.inpcrd --outname comp1

then
mv comp1.top comp1.itp

My comp1.itp file is as following:

; comp1.top created by rdparm2gmx.pl Mon Sep 5 12:45:09 CEST 2011

[ defaults ]

; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ

1 2 yes 0.5 0.8333

[ atomtypes ]

;name bond_type mass charge ptype sigma epsilon

c3 c3 0. 0. A 3.39967e-01 4.57730e-01

n n 0. 0. A 3.25000e-01 7.11280e-01

ha ha 0. 0. A 2.59964e-01 6.27600e-02

ca ca 0. 0. A 3.39967e-01 3.59824e-01

hn hn 0. 0. A 1.06908e-01 6.56888e-02

hc hc 0. 0. A 2.64953e-01 6.56888e-02

c c 0. 0. A 3.39967e-01 3.59824e-01

o o 0. 0. A 2.95992e-01 8.78640e-01

[ moleculetype ]

; Name nrexcl

solute 3

[ atoms ]

; nr type resnr residue atom cgnr charge mass typeB chargeB

1 o 1 UNK O1 1 -0.58510 16.00

2 o 1 UNK O2 2 -0.47810 16.00

3 o 1 UNK O3 3 -0.47710 16.00

4 n 1 UNK N1 4 -0.47010 14.00

...

[ bonds ]

; ai aj funct r k

4 33 1 1.0090e-01 3.4326e+05

7 26 1 1.0920e-01 2.8225e+05

7 25 1 1.0920e-01 2.8225e+05

7 24 1 1.0920e-01 2.8225e+05

...

[ pairs ]

; ai aj funct

1 33 1

4 36 1

4 34 1

5 33 1

...

[ angles ]

; ai aj ak funct theta cth

5 9 32 1 1.1005e+02 3.8802e+02

5 9 31 1 1.1005e+02 3.8802e+02

5 9 30 1 1.1005e+02 3.8802e+02

5 8 29 1 1.1005e+02 3.8802e+02



[ dihedrals ]

;i j k l func C0 ... C5

1 6 4 33 3 29.28800 -8.36800 -20.92000 0.0 0.0 0.0 ;

4 12 17 36 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ;

4 12 14 34 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ;

5 6 4 33 3 20.92000 0.0 -20.92000 0.0 0.0 0.0 ;

6 5 9 32 3 0.65270 1.95811 0.0 -2.61082 0.0 0.0 ;

..

[ system ]

40 system

[ molecules ]

; Compound nmols

solute 1

 

I pasted the coordinates of comp1.pdb into those of protein.pdb, II 
removed directives [ system ] and [ molecules ] and I included 
"comp1.itp" in the "topol.top" file obtained with pdb2gmx (Gromacs 
4.5.4) using ff Amber99SB, on the protein alone:


topol.top:

; Include forcefield parameters

#include "amber99sb.ff/forcefield.itp"

#include "comp1.itp"

; Include chain topologies

#include "topol_Protein_chain_C.itp"

#include "topol_Other.itp"

; Include water topology

#include "amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "amber99sb.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Protein_chain_C 1

Other 1

UNK 1

　

Then, I launched editconf-genbox-grompp to neutralize system:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro 
-o prot-lig_solv.tpr -p


The result was:

Fatal error:

Syntax error - File comp1.itp, line 3

Last line read:

'[ defaults ]'

Invalid order for directive defaults

 

I had a check on the manual and it seems to me that all directives are 
in the correct order! However, I removed




The [defaults] directive can appear only once in a topology and must be the very 
first entry.  There is one in forcefield.itp and then you added another in your 
ligand .itp file.  That's why grompp complains.



directive [ defaults ] and re-launched grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro 
-o prot-lig_solv.tpr -p


Result:

Fatal error:

Syntax error - File comp1.itp, line 7

Last line read:

'[ atomtypes ]'

Invalid order for directive atomtypes

 


I removed directive [ atomtypes ] and re-launched grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro 
-o prot-lig_solv.tpr -p


Result:

Fatal error:

Atomtype n n

[gmx-users] problem in topology with AMBER99SB

[Anna Marabotti]

Dear gmx-users,
I'm trying to create the topology for a ligand using Amber99SB force field,
but I'm experimenting several problems. Here what I did:
 - I recovered the .mol2 file of my ligand (comp1.mol2)
- I checked and added H with Amber tool reduce: reduce comp1.mol2 > comp1-H.
mol2
- I added charges using antechamber: antechamber -i comp1-H.mol2 -fi mol2 -o
comp1-H_C.mol2 -fo mol2 -c bcc -s2
- I created the frcmod parameter file: parmcheck -i comp1-H_C.mol2 -f mol2
-o comp1-H_C.frcmod 
- then I used: xleap -s -f /opt/amber11/dat/leap/cmd/leaprc.ff99SB
source leaprc.gaff
lig = loadmol2 comp1-H_C.mol2
check lig
loadamberparams comp1-H_C.frcmod
saveamberparm lig comp1.prmtop comp1.inpcrd
- I created the .top file with amb2gmx.pl: amb2gmx.pl --prmtop comp1.prmtop
--crd comp1.inpcrd --outname comp1
then
mv comp1.top comp1.itp

My comp1.itp file is as following:

; comp1.top created by rdparm2gmx.pl Mon Sep 5 12:45:09 CEST 2011

[ defaults ]

; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ

1 2 yes 0.5 0.8333

[ atomtypes ]

;name bond_type mass charge ptype sigma epsilon

c3 c3 0. 0. A 3.39967e-01 4.57730e-01

n n 0. 0. A 3.25000e-01 7.11280e-01

ha ha 0. 0. A 2.59964e-01 6.27600e-02

ca ca 0. 0. A 3.39967e-01 3.59824e-01

hn hn 0. 0. A 1.06908e-01 6.56888e-02

hc hc 0. 0. A 2.64953e-01 6.56888e-02

c c 0. 0. A 3.39967e-01 3.59824e-01

o o 0. 0. A 2.95992e-01 8.78640e-01

[ moleculetype ]

; Name nrexcl

solute 3

[ atoms ]

; nr type resnr residue atom cgnr charge mass typeB chargeB

1 o 1 UNK O1 1 -0.58510 16.00

2 o 1 UNK O2 2 -0.47810 16.00

3 o 1 UNK O3 3 -0.47710 16.00

4 n 1 UNK N1 4 -0.47010 14.00


...

[ bonds ]

; ai aj funct r k

4 33 1 1.0090e-01 3.4326e+05

7 26 1 1.0920e-01 2.8225e+05

7 25 1 1.0920e-01 2.8225e+05

7 24 1 1.0920e-01 2.8225e+05


...

[ pairs ]

; ai aj funct

1 33 1

4 36 1

4 34 1

5 33 1


...

[ angles ]

; ai aj ak funct theta cth

5 9 32 1 1.1005e+02 3.8802e+02

5 9 31 1 1.1005e+02 3.8802e+02

5 9 30 1 1.1005e+02 3.8802e+02

5 8 29 1 1.1005e+02 3.8802e+02




[ dihedrals ]

;i j k l func C0 ... C5

1 6 4 33 3 29.28800 -8.36800 -20.92000 0.0 0.0 0.0 ;

4 12 17 36 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ;

4 12 14 34 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ;

5 6 4 33 3 20.92000 0.0 -20.92000 0.0 0.0 0.0 ;

6 5 9 32 3 0.65270 1.95811 0.0 -2.61082 0.0 0.0 ;


..

[ system ]

40 system

[ molecules ]

; Compound nmols

solute 1

 

I pasted the coordinates of comp1.pdb into those of protein.pdb, II removed
directives [ system ] and [ molecules ] and I included "comp1.itp" in the
"topol.top" file obtained with pdb2gmx (Gromacs 4.5.4) using ff Amber99SB,
on the protein alone:

topol.top:

; Include forcefield parameters

#include "amber99sb.ff/forcefield.itp"

#include "comp1.itp"

; Include chain topologies

#include "topol_Protein_chain_C.itp"

#include "topol_Other.itp"

; Include water topology

#include "amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "amber99sb.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Protein_chain_C 1

Other 1

UNK 1

　

Then, I launched editconf-genbox-grompp to neutralize system:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

The result was:

Fatal error:

Syntax error - File comp1.itp, line 3

Last line read:

'[ defaults ]'

Invalid order for directive defaults

 

I had a check on the manual and it seems to me that all directives are in
the correct order! However, I removed directive [ defaults ] and re-launched
grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

Result:

Fatal error:

Syntax error - File comp1.itp, line 7

Last line read:

'[ atomtypes ]'

Invalid order for directive atomtypes

 

I removed directive [ atomtypes ] and re-launched grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

Result:

Fatal error:

Atomtype n not found

　

What's wrong? Why Gromacs claims that directives are not in correct order?
Could you please help me?

Many thanks

Anna

 
__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and 

[gmx-users] Half double pair list method in GROMACS [update]

[ABEL Stephane 175950]

Dear All,

Below a little update and results about the application of half double pair 
list method to scale properly the Coulombic 1-4 interactions in case of a 
system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and GLYCAM06 
(fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined.

I have followed the 4 steps described in [1] and used the following values in 
my forcefield.itp file

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 0.16
#include "ffnonbonded_mod.itp"
;#include "ffnonbonded.itp"
#include "ffbonded.itp"

I used two different topology files for the glycolipid (bDM) and the peptide. 
One with (*_mod.itp) with pair list parameters duplicated 6 times (bDM) and 5 
times (peptide) and with single pair list (*_no_mod.itp) as decribed in [1].

TESTING:

Three 3 different systems were examined:

A. A first system containing 1 glycolipid (bDM)  in water cubic box
B. A second system with 1 peptide in TIP3P water
C. And a third system with 1 peptide and 1 glycolipid in water cubic box

To obtain the glycolipid and peptide energy pairs, I did one step of MD in NVT 
ensemble with the *.mdp file given in [2] with different energygrps and tc_grps.
For 1. energygrps and tc_grps = bDM SOL
For 2. energygrps and tc_grps = Protein SOL
For 3. energygrps and = Protein bDM SOL

bDM/water system

Test_A1

## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and  the 
*_no_mod.itp file :
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 1.0 1.0
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02

Test_A2

 with the topology *_mod.itp file and the directive
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 1.0 0.16
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
bDM-bDM   -4.00855e+02   -3.71401e+012.03406e+032.79234e+02

Test_A3

 with the topology *_no_mod.itp file and the directive
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 1.0 0.16
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
bDM-bDM   -4.00855e+02   -3.71401e+013.39010e+022.79234e+02

Coul-14 energy for bDM-bDM in Test_A1 = Coul-14 energy in Test_A2 --> OK !
Coul-14 energy for bDM-bDM Test_A3 is 6 smaller than Coul-14 energy in Test_A1 
and Test 2 ---> OK !

peptide/water system

Test_B1

 Control with AMBER force field fudgeLJ fudgeQQ parameters, the 
*_no_mod.itp file
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 0.5  0.8333
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
Protein-Protein   -1.49026e+03   -4.12114e+023.80551e+036.55321e+02

Test_B2

 Control with the peptide *_no_mod.itp file and the directive
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 1.0 0.166
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
Protein-Protein   -1.49026e+03   -4.12114e+027.61132e+021.31064e+03

Test_B3

 With the peptide *_mod.itp file and the directive
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
##  1   2   yes 1.0 0.16
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
Protein-Protein   -1.49026e+03   -4.12114e+023.80566e+036.55320e+02

Coul-14 and LJ-14 energies for Protein-Protein in Test_B3 are 5 times Coul-14 
and 2 times LJ-14 energies, respectively, than in Test_B1 ---> OK !
Coul-14 and LJ-14 energies for Protein-Protein in Test_B3 = Coul-14 and LJ-14 
energies in Test_B1 ---> OK !

peptide/bDM/water system

Test_C1

## Control with the peptide and the bDM *_mod.itp topology files and the 
directive
##; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
## 1   2   yes 1.0 0.16
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
Protein-Protein   -1.48386e+03   -3.99146e+023.79532e+036.53553e+02
bDM-bDM   -3.69788e+02   -3.51804e+012.00228e+032.25026e+02

Test_C2

## Control with the peptide and the bDM *no_mod.itp topology files and  the 
directive
Epot (kJ/mol)Coul-SR  LJ-SRCoul-14  LJ-14
Protein-Protein   -1.48386e+03   -3.99146e+027.59063e+021.30711e+03
bDM-bDM   -3.69788e+02   -3.51804e+013.33713e+022.25026e+02

bDM-bDM Coul-14 energy in Test_C2 is 6 times smaller, respectively, than in the 
Test_C1  ---> OK !
Protein-Protein Coul-14 and LJ1-4

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

[J. Nathan Scott]

On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham wrote:

>  On 6/09/2011 1:22 AM, J. Nathan Scott wrote:
>
>
>
> On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote:
>
>>  On 5/09/2011 3:30 AM, J. Nathan Scott wrote:
>>
>>> Hello fellow GROMACS users,
>>>
>>> I am in the process of constructing a new residue in the OPLS-AA force
>>> field for the mCherry chromophore. However, I am having some difficulty in
>>> adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore
>>> residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended
>>> chain carbon named CE. The problem is that my hdb rules were assigning HE1
>>> and HE2 to the ring carbon hydrogens (1   1   HE1 CE1 CD1
>>>   CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3
>>> 4   HE CE SD  CG1). Since these hydrogens are of different
>>> types, I need to have them named distinctly in my RTP file and need for
>>> Gromacs to understand them as different types. I changed the CH6 residue's
>>> CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see
>>> below). I also changed the hdb entry for the new CE3 atom (also below).
>>>
>>> Relevant RTP lines:
>>>   CE3opls_209  0.0 10
>>>  HE31opls_140  0.0 11
>>>  HE32opls_140  0.0 12
>>>  HE33opls_140  0.0 13
>>>   CE1opls_145  0.0 32
>>>   HE1opls_146  0.0 33
>>>   CE2opls_145  0.0 34
>>>   HE2opls_146  0.0 35
>>>  [bonds]
>>>   CE3  HE31
>>>   CE3  HE32
>>>   CE3  HE33
>>>   CE1   HE1
>>>   CE2   HE2
>>>
>>> Relevant HDB lines:
>>> 3   4   HE3 CE3 SD  CG1
>>> 1   1   HE1 CE1 CD1 CZ
>>> 1   1   HE2 CE2 CD2 CZ
>>>
>>> I thought this would cover everything, but I am receiving the following
>>> sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx
>>> -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3):
>>>
>>> "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
>>> You might need to add atom HE31 to the hydrogen database of
>>> building block CH6
>>> in the file aminoacids.hdb (see the manual)"
>>>
>>> I've looked at other examples in the aminoacids.hdb file and cannot
>>> figure out what I am missing here, it seems like my hdb rule should be
>>> adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the
>>> other hdb rules are OK, since they seemed to work fine before, as indicated
>>> by examining the gro file. I would sincerely appreciate any help you can
>>> offer. Thank you!
>>>
>>
>>  I can't see a reason why that wouldn't work. However, there's no need
>> for you to preserve the PDB atom name for CE. Reducing the potential for
>> some atom-naming screw-up such as this is a good reason to change it (in
>> both your coordinate file and .rtp entry). It will probably just work, or at
>> the very least simplify further trouble-shooting.
>>
>> Mark
>>
>
> Hello Mark, thank you for your help, but I took your very reasonable advice
> and am still receiving the exact same sort of error. I changed the PDB file
> atom name to CQ, which of course makes it unique within that residue (and
> indeed in the whole PDB file). I updated my .rtp entries and the .hdb rules
> accordingly, and yet I still receive the exact same sort of error. It seems
> as if something is wrong with my hdb syntax, but having looked at numerous
> other examples in the hdb file and online I am at a loss as to what the
> problem might be. For what it's worth, if I use the -missing switch when I
> run pdb2gmx, the other CH6 hydrogen atoms appear to be added correctly in
> the resulting gro file, with the names exactly as I expected from the hdb
> naming rules.
>
>
> My input:
> pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3
>
> Error received:
> "WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
>  You might need to add atom HQ1 to the hydrogen database of
> building block CH6
>  in the file aminoacids.hdb (see the manual)"
>
> "WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
>  You might need to add atom HQ1 to the hydrogen database of
> building block CH6
>  in the file aminoacids.hdb (see the manual)"
>
> "WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file
>  You might need to add atom HQ1 to the hydrogen database of
> building block CH6
>  in the file aminoacids.hdb (see the manual)"
>
>
>
> PDB file:
> ATOM493  CQ  CH6 A  66  42.848  20.230   6.798  1.00 40.19
>
> hdb file:
> CH6 9
> 2   6   HG1 CG1 SD  CB1
> 2   6   HB1 CB1 CG1 CA1
> 2   6   HA3 CA3 C3  N3
> 1   1   HB2 CB2 CA2 CG2
> 1   1   HD1 CD1 CE1 CG2
> 1   1   HD2 CD2 CE2 CG2
> 1   1   HE1 CE1 CD1 CZ
> 1   1   HE2 CE2 CD2

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

[Mark Abraham]

On 6/09/2011 1:22 AM, J. Nathan Scott wrote:



On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham > wrote:


On 5/09/2011 3:30 AM, J. Nathan Scott wrote:

Hello fellow GROMACS users,

I am in the process of constructing a new residue in the
OPLS-AA force field for the mCherry chromophore. However, I am
having some difficulty in adding three CH3 hydrogens. In the
2H5Q PDB structure the chromophore residue, CH6, has CE1 and
CE2 ring carbons defined, but also an extended chain carbon
named CE. The problem is that my hdb rules were assigning HE1
and HE2 to the ring carbon hydrogens (1   1   HE1
CE1 CD1 CZ for example), and HE1, HE2, and HE3 to the
CE carbon hydrogens (3   4   HE CE SD
 CG1). Since these hydrogens are of different types, I need to

have them named distinctly in my RTP file and need for Gromacs
to understand them as different types. I changed the CH6
residue's CE atom to CE3 in the PDB file and the relevant RTP
entries accordingly (see below). I also changed the hdb entry
for the new CE3 atom (also below).

Relevant RTP lines:
  CE3opls_209  0.0 10
 HE31opls_140  0.0 11
 HE32opls_140  0.0 12
 HE33opls_140  0.0 13
  CE1opls_145  0.0 32
  HE1opls_146  0.0 33
  CE2opls_145  0.0 34
  HE2opls_146  0.0 35
 [bonds]
  CE3  HE31
  CE3  HE32
  CE3  HE33
  CE1   HE1
  CE2   HE2

Relevant HDB lines:
3   4   HE3 CE3 SD  CG1
1   1   HE1 CE1 CD1 CZ
1   1   HE2 CE2 CD2 CZ

I thought this would cover everything, but I am receiving the
following sort of error from pdb2gmx for each of the the three
CE3 hydrogens(pdb2gmx -f 2H5Q.pdb -o 2H5Q_processed.gro -water
tip3):

"WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
You might need to add atom HE31 to the hydrogen
database of building block CH6
in the file aminoacids.hdb (see the manual)"

I've looked at other examples in the aminoacids.hdb file and
cannot figure out what I am missing here, it seems like my hdb
rule should be adding 3 type 4 hydrogens named HE31, HE32, and
HE33. I am assuming that the other hdb rules are OK, since
they seemed to work fine before, as indicated by examining the
gro file. I would sincerely appreciate any help you can offer.
Thank you!


I can't see a reason why that wouldn't work. However, there's no
need for you to preserve the PDB atom name for CE. Reducing the
potential for some atom-naming screw-up such as this is a good
reason to change it (in both your coordinate file and .rtp entry).
It will probably just work, or at the very least simplify further
trouble-shooting.

Mark


Hello Mark, thank you for your help, but I took your very reasonable 
advice and am still receiving the exact same sort of error. I changed 
the PDB file atom name to CQ, which of course makes it unique within 
that residue (and indeed in the whole PDB file). I updated my .rtp 
entries and the .hdb rules accordingly, and yet I still receive the 
exact same sort of error. It seems as if something is wrong with my 
hdb syntax, but having looked at numerous other examples in the hdb 
file and online I am at a loss as to what the problem might be. For 
what it's worth, if I use the -missing switch when I run pdb2gmx, the 
other CH6 hydrogen atoms appear to be added correctly in the resulting 
gro file, with the names exactly as I expected from the hdb naming rules.



My input:
pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3

Error received:
"WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of 
building block CH6

 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of 
building block CH6

 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of 
building block CH6

 in the file aminoacids.hdb (see the manual)"



PDB file:
ATOM493  CQ  CH6 A  66  42.848  20.230   6.798  1.00 40.19

hdb file:
CH6 9
2   6   HG1 CG1 SD  CB1
2   6   HB1 CB1 CG1 CA1
2   6   HA3 CA3 C3  N3
1   1   HB2 CB2 CA2 CG2
1   1   HD1 CD1 CE1 CG2
1   

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

[J. Nathan Scott]

On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote:

> On 5/09/2011 3:30 AM, J. Nathan Scott wrote:
>
>> Hello fellow GROMACS users,
>>
>> I am in the process of constructing a new residue in the OPLS-AA force
>> field for the mCherry chromophore. However, I am having some difficulty in
>> adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore
>> residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended
>> chain carbon named CE. The problem is that my hdb rules were assigning HE1
>> and HE2 to the ring carbon hydrogens (1   1   HE1 CE1 CD1
>>   CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3
>> 4   HE CE SD  CG1). Since these hydrogens are of different
>> types, I need to have them named distinctly in my RTP file and need for
>> Gromacs to understand them as different types. I changed the CH6 residue's
>> CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see
>> below). I also changed the hdb entry for the new CE3 atom (also below).
>>
>> Relevant RTP lines:
>>   CE3opls_209  0.0 10
>>  HE31opls_140  0.0 11
>>  HE32opls_140  0.0 12
>>  HE33opls_140  0.0 13
>>   CE1opls_145  0.0 32
>>   HE1opls_146  0.0 33
>>   CE2opls_145  0.0 34
>>   HE2opls_146  0.0 35
>>  [bonds]
>>   CE3  HE31
>>   CE3  HE32
>>   CE3  HE33
>>   CE1   HE1
>>   CE2   HE2
>>
>> Relevant HDB lines:
>> 3   4   HE3 CE3 SD  CG1
>> 1   1   HE1 CE1 CD1 CZ
>> 1   1   HE2 CE2 CD2 CZ
>>
>> I thought this would cover everything, but I am receiving the following
>> sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx
>> -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3):
>>
>> "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
>> You might need to add atom HE31 to the hydrogen database of
>> building block CH6
>> in the file aminoacids.hdb (see the manual)"
>>
>> I've looked at other examples in the aminoacids.hdb file and cannot figure
>> out what I am missing here, it seems like my hdb rule should be adding 3
>> type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the other
>> hdb rules are OK, since they seemed to work fine before, as indicated by
>> examining the gro file. I would sincerely appreciate any help you can offer.
>> Thank you!
>>
>
> I can't see a reason why that wouldn't work. However, there's no need for
> you to preserve the PDB atom name for CE. Reducing the potential for some
> atom-naming screw-up such as this is a good reason to change it (in both
> your coordinate file and .rtp entry). It will probably just work, or at the
> very least simplify further trouble-shooting.
>
> Mark
>

Hello Mark, thank you for your help, but I took your very reasonable advice
and am still receiving the exact same sort of error. I changed the PDB file
atom name to CQ, which of course makes it unique within that residue (and
indeed in the whole PDB file). I updated my .rtp entries and the .hdb rules
accordingly, and yet I still receive the exact same sort of error. It seems
as if something is wrong with my hdb syntax, but having looked at numerous
other examples in the hdb file and online I am at a loss as to what the
problem might be. For what it's worth, if I use the -missing switch when I
run pdb2gmx, the other CH6 hydrogen atoms appear to be added correctly in
the resulting gro file, with the names exactly as I expected from the hdb
naming rules.


My input:
pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3

Error received:
"WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of building
block CH6
 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of building
block CH6
 in the file aminoacids.hdb (see the manual)"

"WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file
 You might need to add atom HQ1 to the hydrogen database of building
block CH6
 in the file aminoacids.hdb (see the manual)"



PDB file:
ATOM493  CQ  CH6 A  66  42.848  20.230   6.798  1.00 40.19

hdb file:
CH6 9
2   6   HG1 CG1 SD  CB1
2   6   HB1 CB1 CG1 CA1
2   6   HA3 CA3 C3  N3
1   1   HB2 CB2 CA2 CG2
1   1   HD1 CD1 CE1 CG2
1   1   HD2 CD2 CE2 CG2
1   1   HE1 CE1 CD1 CZ
1   1   HE2 CE2 CD2 CZ
3   4   HQ  CQ  SD  CG1

rtp file (relevant portions only):
CQopls_209  0.0 10
   HQ1opls_140  0.0 11
   HQ2opls_140  0.0 12
   HQ3opls_140  0.0 13
[bonds]
SD CQ
CQ   HQ

Re: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

[Justin A. Lemkul]

Jackson Chief wrote:
I want to make a model of a GPCR inserted into lipid bilayer.  I 
obtained the structure file for a solvated POPC bilayer from the 
CHARMM-GUI site.  I used CHARMM27 force field to model the bilayer 
and *pdb2gmx *had no problem generating the *.gro, *.top, and posre.itp 
files.  When I perform *grompp* I receive the following warning and error;


"WARNING 1 [file ffnonbonded.itp, line 130]:
  Overriding atomtype HOL"



Here you have an atomtype defined twice somehow.


"ERROR 1 [file bilayer.top, line 271489]:
  No default U-B types"



This error suggests you've created a bonded interaction for which parameters do 
not exist, probably through use of incorrect atom types.


I though that the issue with creating Urey-Bradley interactions 
using *pdb2gmx *had been corrected in Gromacs-4.5.4.  Please give me 
some advice on how to proceed further.


To what issue are you referring?

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

[Jackson Chief]

I want to make a model of a GPCR inserted into lipid bilayer.  I obtained
the structure file for a solvated POPC bilayer from the CHARMM-GUI site.  I
used CHARMM27 force field to model the bilayer and *pdb2gmx *had no problem
generating the *.gro, *.top, and posre.itp files.  When I perform *grompp* I
receive the following warning and error;

"WARNING 1 [file ffnonbonded.itp, line 130]:
  Overriding atomtype HOL"

"ERROR 1 [file bilayer.top, line 271489]:
  No default U-B types"

I though that the issue with creating Urey-Bradley interactions using *pdb2gmx
*had been corrected in Gromacs-4.5.4.  Please give me some advice on how to
proceed further.

Thank you,
Jackson Chief Elk
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Re: [gmx-users] Error from residues added to rtp file

[Delmotte, Antoine]

This solved my problem, although I am not totally sure to have perfectly 
understood how the .tdb had to be edited. I added the following entry:


[ MME-NH ]
[ delete ]
H

Anyway, it solved the problem I had.

Many thanks for your help!

Antoine

On 09/05/2011 09:54 AM, Mark Abraham wrote:

On 5/09/2011 6:41 PM, Delmotte, Antoine wrote:

Dear Gromacs users,

I am once again requesting your help for the editing of the opls 
force field .rtp and .hdb files.


I have inserted the parameters for a new residue, N-methyl methionine 
(MME). In this molecule, the methyl group is attached to the nitrogen 
atom from the peptide bond, which I think is the origin of my problem.


pdb2gmx works fine and generates the topology files without any 
error. Unfortunately, when I looked at the .gro file generated in 
PyMol (after conversion to pdb with g_editconf), I realized that 3 
hydrogens have been added to the nitrogen atom, so I effectively get 
R2-N-H4:


H1 \   / CH3
H2 - N - CA - (rest of the aminoa acid)...
H3 /   \ H

instead of R2-N-H:

CH3 \
  N - CA - (rest of the aminoa acid)...
  H /

My guess is that Gromacs automatically adds those 3 hydrogens because 
MME is a terminal residue, but I don't know how to prevent pdb2gmx 
from doing so.


That uses the .tdb terminal database system. You will need a custom 
entry to generate your two hydrogen atoms, and to use pdb2gmx -ter to 
get a chance to select it.


Separately, if this residue is ever to be a non-terminal one, you'll 
need to define one H atom bound to the N atom in the .rtp entry, so do 
that now.


Mark



I have tried different modifications in the .rtp file, including 
using different atom types, removing the peptide bond (the line N -C 
) in the list of bonds, changing the hdb file, but nothing seems to 
have had any effect.


I guess I could also simply remove these hydrogens from the .gro and 
.itp files after using pdb2gmx, but I would have a better confidence 
in what I changed in the force field files if pdb2gmx was giving me 
the right answer directly.


See below my .rtp and .hdb entries:

[ MME ]
 [ atoms ]
 Nopls_238   -0.500 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_136   -0.120 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
CGopls_2100.048 3
   HG1opls_1400.060 3
   HG2opls_1400.060 3
SDopls_202   -0.335 4
CEopls_209   -0.013 5
   HE1opls_1400.060 5
   HE2opls_1400.060 5
   HE3opls_1400.060 5
 Copls_2350.500 6
 Oopls_236   -0.500 6
CMopls_244   -0.110 7
   HM1opls_1400.037 7
   HM2opls_1400.037 7
   HM3opls_1400.037 7
 [ bonds ]
 NCA
 NCM
CM   HM1
CM   HM2
CM   HM3
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGSD
SDCE
CE   HE1
CE   HE2
CE   HE3
 C O

MME 6
1   1   H   N   CM  CA
1   5   HA  CA  N   C   CB
2   6   HB  CB  CG  CA
2   6   HG  CG  SD  CB
3   4   HE  CE  SD  CG
3   4   HM  CM  N   CA

Once again, any idea about this problem would be greatly appreciated.

Thanks to all in advance.

Regards,

Antoine


On 08/26/2011 05:42 PM, Delmotte, Antoine wrote:

Oh, thank you so much! That was indeed the error.

It's amazing how these little things can sometimes drive you mad

Thanks a lot,

Antoine

On 08/26/2011 05:27 PM, Thomas Piggot wrote:

Hi,

I think the problem is that you have a dash rather than a minus
symbol for the sign of the charge on the OD atom.

Cheers

Tom

Delmotte, Antoine wrote:

Dear Gromacs users,

I am currently trying to run an MD simulation with the OPLS-AA 
force field on a protein having different non standard residues 
and a ligand. I found the charges for the OPLS force field for 
these residues in the literature and I am now trying to add them 
in the OPLS force field parameter files.


I have edited the aminoacids.rtp and the aminoacids.hdb files for 
the OPLS-AA force field, as well as the residuetypes.dat file. 
Here is an example for one of the amino acids, hydroxyproline:


[ HYP ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.120 3
HG1 opls_140 0.060 3
OD opls_167 −0.683 3
HD opls_168 0.743 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG OD
OD HD
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y


When I run pdb2gmx, I get the following error, which is not very 
informative:


All occupancies are one
Opening force field file 
/

Re: [gmx-users] Error from residues added to rtp file

[Mark Abraham]

On 5/09/2011 6:41 PM, Delmotte, Antoine wrote:

Dear Gromacs users,

I am once again requesting your help for the editing of the opls force 
field .rtp and .hdb files.


I have inserted the parameters for a new residue, N-methyl methionine 
(MME). In this molecule, the methyl group is attached to the nitrogen 
atom from the peptide bond, which I think is the origin of my problem.


pdb2gmx works fine and generates the topology files without any error. 
Unfortunately, when I looked at the .gro file generated in PyMol 
(after conversion to pdb with g_editconf), I realized that 3 hydrogens 
have been added to the nitrogen atom, so I effectively get R2-N-H4:


H1 \   / CH3
H2 - N - CA - (rest of the aminoa acid)...
H3 /   \ H

instead of R2-N-H:

CH3 \
  N - CA - (rest of the aminoa acid)...
  H /

My guess is that Gromacs automatically adds those 3 hydrogens because 
MME is a terminal residue, but I don't know how to prevent pdb2gmx 
from doing so.


That uses the .tdb terminal database system. You will need a custom 
entry to generate your two hydrogen atoms, and to use pdb2gmx -ter to 
get a chance to select it.


Separately, if this residue is ever to be a non-terminal one, you'll 
need to define one H atom bound to the N atom in the .rtp entry, so do 
that now.


Mark



I have tried different modifications in the .rtp file, including using 
different atom types, removing the peptide bond (the line N -C ) in 
the list of bonds, changing the hdb file, but nothing seems to have 
had any effect.


I guess I could also simply remove these hydrogens from the .gro and 
.itp files after using pdb2gmx, but I would have a better confidence 
in what I changed in the force field files if pdb2gmx was giving me 
the right answer directly.


See below my .rtp and .hdb entries:

[ MME ]
 [ atoms ]
 Nopls_238   -0.500 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_136   -0.120 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
CGopls_2100.048 3
   HG1opls_1400.060 3
   HG2opls_1400.060 3
SDopls_202   -0.335 4
CEopls_209   -0.013 5
   HE1opls_1400.060 5
   HE2opls_1400.060 5
   HE3opls_1400.060 5
 Copls_2350.500 6
 Oopls_236   -0.500 6
CMopls_244   -0.110 7
   HM1opls_1400.037 7
   HM2opls_1400.037 7
   HM3opls_1400.037 7
 [ bonds ]
 NCA
 NCM
CM   HM1
CM   HM2
CM   HM3
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGSD
SDCE
CE   HE1
CE   HE2
CE   HE3
 C O

MME 6
1   1   H   N   CM  CA
1   5   HA  CA  N   C   CB
2   6   HB  CB  CG  CA
2   6   HG  CG  SD  CB
3   4   HE  CE  SD  CG
3   4   HM  CM  N   CA

Once again, any idea about this problem would be greatly appreciated.

Thanks to all in advance.

Regards,

Antoine


On 08/26/2011 05:42 PM, Delmotte, Antoine wrote:

Oh, thank you so much! That was indeed the error.

It's amazing how these little things can sometimes drive you mad

Thanks a lot,

Antoine

On 08/26/2011 05:27 PM, Thomas Piggot wrote:

Hi,

I think the problem is that you have a dash rather than a minus 
symbol for the sign of the charge on the OD atom.


Cheers

Tom

Delmotte, Antoine wrote:

Dear Gromacs users,

I am currently trying to run an MD simulation with the OPLS-AA 
force field on a protein having different non standard residues and 
a ligand. I found the charges for the OPLS force field for these 
residues in the literature and I am now trying to add them in the 
OPLS force field parameter files.


I have edited the aminoacids.rtp and the aminoacids.hdb files for 
the OPLS-AA force field, as well as the residuetypes.dat file. Here 
is an example for one of the amino acids, hydroxyproline:


[ HYP ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.120 3
HG1 opls_140 0.060 3
OD opls_167 −0.683 3
HD opls_168 0.743 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG OD
OD HD
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y


When I run pdb2gmx, I get the following error, which is not very 
informative:


All occupancies are one
Opening force field file 
/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp

Atomtype 1
Reading residue database... (oplsaa)
Opening force field file 
/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp

Residue 58
---
Program g_pdb2gmx, VERSION 4.5.3
Source code file: 
/

Re: [gmx-users] Error from residues added to rtp file

[Delmotte, Antoine]

Dear Gromacs users,

I am once again requesting your help for the editing of the opls force 
field .rtp and .hdb files.


I have inserted the parameters for a new residue, N-methyl methionine 
(MME). In this molecule, the methyl group is attached to the nitrogen 
atom from the peptide bond, which I think is the origin of my problem.


pdb2gmx works fine and generates the topology files without any error. 
Unfortunately, when I looked at the .gro file generated in PyMol (after 
conversion to pdb with g_editconf), I realized that 3 hydrogens have 
been added to the nitrogen atom, so I effectively get R2-N-H4:


H1 \   / CH3
H2 - N - CA - (rest of the aminoa acid)...
H3 /   \ H

instead of R2-N-H:

CH3 \
  N - CA - (rest of the aminoa acid)...
  H /

My guess is that Gromacs automatically adds those 3 hydrogens because 
MME is a terminal residue, but I don't know how to prevent pdb2gmx from 
doing so.


I have tried different modifications in the .rtp file, including using 
different atom types, removing the peptide bond (the line N -C ) in the 
list of bonds, changing the hdb file, but nothing seems to have had any 
effect.


I guess I could also simply remove these hydrogens from the .gro and 
.itp files after using pdb2gmx, but I would have a better confidence in 
what I changed in the force field files if pdb2gmx was giving me the 
right answer directly.


See below my .rtp and .hdb entries:

[ MME ]
 [ atoms ]
 Nopls_238   -0.500 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_136   -0.120 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
CGopls_2100.048 3
   HG1opls_1400.060 3
   HG2opls_1400.060 3
SDopls_202   -0.335 4
CEopls_209   -0.013 5
   HE1opls_1400.060 5
   HE2opls_1400.060 5
   HE3opls_1400.060 5
 Copls_2350.500 6
 Oopls_236   -0.500 6
CMopls_244   -0.110 7
   HM1opls_1400.037 7
   HM2opls_1400.037 7
   HM3opls_1400.037 7
 [ bonds ]
 NCA
 NCM
CM   HM1
CM   HM2
CM   HM3
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGSD
SDCE
CE   HE1
CE   HE2
CE   HE3
 C O

MME 6
1   1   H   N   CM  CA
1   5   HA  CA  N   C   CB
2   6   HB  CB  CG  CA
2   6   HG  CG  SD  CB
3   4   HE  CE  SD  CG
3   4   HM  CM  N   CA

Once again, any idea about this problem would be greatly appreciated.

Thanks to all in advance.

Regards,

Antoine


On 08/26/2011 05:42 PM, Delmotte, Antoine wrote:

Oh, thank you so much! That was indeed the error.

It's amazing how these little things can sometimes drive you mad

Thanks a lot,

Antoine

On 08/26/2011 05:27 PM, Thomas Piggot wrote:

Hi,

I think the problem is that you have a dash rather than a minus 
symbol for the sign of the charge on the OD atom.


Cheers

Tom

Delmotte, Antoine wrote:

Dear Gromacs users,

I am currently trying to run an MD simulation with the OPLS-AA force 
field on a protein having different non standard residues and a 
ligand. I found the charges for the OPLS force field for these 
residues in the literature and I am now trying to add them in the 
OPLS force field parameter files.


I have edited the aminoacids.rtp and the aminoacids.hdb files for 
the OPLS-AA force field, as well as the residuetypes.dat file. Here 
is an example for one of the amino acids, hydroxyproline:


[ HYP ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.120 3
HG1 opls_140 0.060 3
OD opls_167 −0.683 3
HD opls_168 0.743 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG OD
OD HD
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y


When I run pdb2gmx, I get the following error, which is not very 
informative:


All occupancies are one
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file 
/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp

Residue 58
---
Program g_pdb2gmx, VERSION 4.5.3
Source code file: 
/builddir/build/BUILD/gromacs-4.5.3/src/kernel/resall.c, line: 389


Fatal error:
in .rtp file in residue HYP at line:
OD opls_167 −0.683 3


I would be grateful if anyone could shed some light on the origin of 
this error, and on what I can do to correct it.


I am using Gromacs 4.5.3.

Thanks a lot in advance,

Antoine










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