Re: [gmx-users] Error in hdb file ffG43a1p.hdb

[Mark Abraham]

Thamu wrote:

Hi,

i am trying to run md for protein-peptide complex. the peptide has
phosphorylated tyrosine.

i got the following error when i run pdb2gmx

Fatal error:
Error in hdb file ffG43a1p.hdb:
Wrong number of control atoms (2 iso 3) on line:
11N-CCA


I would greatly appreciate if some one help me to solve this error.


Read each dot point in section 5.6.2. You've omitted a necessary field.

Mark
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Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

[Mark Abraham]

Lanyuan Lu wrote:
> Hi Mark,
> Thanks for your reply. Yes, I did save velocities in the same frequency 
> as positions. And the length of two compared trajectories are exactly 
> the same. I think I've figured it out and I did looked at the average 
> values as the output of the g_energy. It seems the number 545.384 from 
> the original MD edr file is incorrect. I opened the xvg file in xmgrace 
> and found the average pressure should be 1153.22, which is close to the 
> rerun result. I used the command "g_energy -f *.edr -o *.xvg" to dump 
> the pressure from two edr files and found both of the two xvg files have 
> time from 0 ps to 200 ps with 201 frames. I also found for each time 
> step the pressure values are close for the two files. Therefore, I don't 
> understand why I got the incorrect average pressure from the original 
> edr output, while the rerun output was correct. Another test I did was 
> to type "g_energy -f *.edr -o *.xvg -b 100" to get the last 100 ps 
> results. And this time the average number from the original edr file is 
> still incorrect. However, just as in the whole 200 ps case, I can get 
> the right number if I manually calculate the average from the xvg file.
> Lanyuan

Hence...

>> Did your primary mdrun include an
>> equilibration period that the rerun did not?

See appendix C.2. The averages reported by g_energy are not necessarily
the averages of the data in the file. You can see whether this is
happening by comparing a gmxdump of the two .edr files, or using the
gmxcheck facility for comparing them. Assuming that your original mdrun
was pre-equilibrated, I expect you will see the partial sums are
different at each step - and the first one in particular.

Mark
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[gmx-users] Error in hdb file ffG43a1p.hdb

[Thamu]

Hi,

i am trying to run md for protein-peptide complex. the peptide has
phosphorylated tyrosine.

i got the following error when i run pdb2gmx

Fatal error:
Error in hdb file ffG43a1p.hdb:
Wrong number of control atoms (2 iso 3) on line:
11N-CCA


I would greatly appreciate if some one help me to solve this error.

Thanking you,

Yours sincerely,
Thamu
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Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

[Lanyuan Lu]

Hi Mark,
Thanks for your reply. Yes, I did save velocities in the same frequency as 
positions. And the length of two compared trajectories are exactly the same. 
I think I've figured it out and I did looked at the average values as the 
output of the g_energy. It seems the number 545.384 from the original MD edr 
file is incorrect. I opened the xvg file in xmgrace and found the average 
pressure should be 1153.22, which is close to the rerun result. I used the 
command "g_energy -f *.edr -o *.xvg" to dump the pressure from two edr files 
and found both of the two xvg files have time from 0 ps to 200 ps with 201 
frames. I also found for each time step the pressure values are close for 
the two files. Therefore, I don't understand why I got the incorrect average 
pressure from the original edr output, while the rerun output was correct. 
Another test I did was to type "g_energy -f *.edr -o *.xvg -b 100" to get 
the last 100 ps results. And this time the average number from the original 
edr file is still incorrect. However, just as in the whole 200 ps case, I 
can get the right number if I manually calculate the average from the xvg 
file.

Lanyuan

- Original Message - 
From: "Mark Abraham" 

To: "Discussion list for GROMACS users" 
Sent: Thursday, July 23, 2009 7:55 PM
Subject: Re: [gmx-users] Wrong pressure with "mdrun -rerun" option



LuLanyuan wrote:

Hello all,
From the notes for gmx 4.0.5, the pressure and virial from "-rerun" 
should be correct. However, I did a test for a box of tip3p water and 
found the pressure results from rerun were different compared to the 
original results. For the first MD simulation , I simulated it for 200 ps 
and use the neighbor list update frequency 1. I used "g_energy" to 
extract pressure results and the results were 545.384 and 1153.55 bars 
for the MD and rerun, respectively. The gromacs version is 4.0.5.


Did you save velocities suitably? Did your primary mdrun include an
equilibration period that the rerun did not? Are you quoting average
pressures?

Mark
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Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

[Mark Abraham]

LuLanyuan wrote:
> Hello all,
>>From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be 
>>correct. However, I did a test for a box of tip3p water and found the 
>>pressure results from rerun were different compared to the original results. 
>>For the first MD simulation , I simulated it for 200 ps and use the neighbor 
>>list update frequency 1. I used "g_energy" to extract pressure results and 
>>the results were 545.384 and 1153.55 bars for the MD and rerun, respectively. 
>>The gromacs version is 4.0.5.

Did you save velocities suitably? Did your primary mdrun include an
equilibration period that the rerun did not? Are you quoting average
pressures?

Mark
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Re: [gmx-users] genconf

[Justin A. Lemkul]

Payman Pirzadeh wrote:

Hi Justin,
I checked the trjconv help. It also takes .gro files. If so, do I still need
to provide a .tpr file? (if yes, then the output can be .gro?)



Any of the listed file formats can be input or output.  To fix "broken" 
molecules, you must supply a .tpr file.  If you run trjconv without it, you will 
get an error.


-Justin


Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 22, 2009 6:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf




Payman Pirzadeh wrote:

Hello,
I minimized the initial output (from another simulation) first; then I
replicated it. This time, the minimization of the bigger box was done more
easily! I ran an MD simulation with the bigger box and after 6 hours, it

has

not crashed yet.
But, I have a question. When we replicate a box, and in the primary box

one

molecule is dissected into pieces due to pbc, will GROMACS return the
molecules to its original shape during MD run or not?


No, it does not.


I believe, without minimization, these dissected pieces will remain in the
middle of the box and interfere with their replicated versions. Maybe,
'genconf' should be modified for such replications to maintain the pbc
between the new molecules at the boundaries and fix the problem with the
particle in the middle of the new bigger box!



It can easily be accomplished using a .tpr file, and by using trjconv -pbc 
whole.  After molecules are whole, then use genconf.


-Justin

Payman 


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 22, 2009 9:22 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] genconf

Thanks a lot Mark! I will run the system for equilibration and then try to
replicate it. I will keep you guys posted.

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: July 21, 2009 11:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf

Payman Pirzadeh wrote:

Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal

structure

is maintained under pbc?
Can the option "-dist" help here?
Replicating a box that was not designed for periodicity will always have 
this problem. Whether the box is too small or two large, there will 
either be steric clashes, or vacuums that will need filling. The general 
solution is to equilibrate your box under PBC prior to replication. Now 
the box size and the atomic spacings will be plausible, and the 
replication will not of necessity introduce artifacts.


Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] genconf

[Payman Pirzadeh]

Hi Justin,
I checked the trjconv help. It also takes .gro files. If so, do I still need
to provide a .tpr file? (if yes, then the output can be .gro?)

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 22, 2009 6:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf




Payman Pirzadeh wrote:
> Hello,
> I minimized the initial output (from another simulation) first; then I
> replicated it. This time, the minimization of the bigger box was done more
> easily! I ran an MD simulation with the bigger box and after 6 hours, it
has
> not crashed yet.
> But, I have a question. When we replicate a box, and in the primary box
one
> molecule is dissected into pieces due to pbc, will GROMACS return the
> molecules to its original shape during MD run or not?

No, it does not.

> I believe, without minimization, these dissected pieces will remain in the
> middle of the box and interfere with their replicated versions. Maybe,
> 'genconf' should be modified for such replications to maintain the pbc
> between the new molecules at the boundaries and fix the problem with the
> particle in the middle of the new bigger box!
> 

It can easily be accomplished using a .tpr file, and by using trjconv -pbc 
whole.  After molecules are whole, then use genconf.

-Justin

> Payman 
> 
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Payman Pirzadeh
> Sent: July 22, 2009 9:22 AM
> To: 'Discussion list for GROMACS users'
> Subject: RE: [gmx-users] genconf
> 
> Thanks a lot Mark! I will run the system for equilibration and then try to
> replicate it. I will keep you guys posted.
> 
> Payman
> 
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Mark Abraham
> Sent: July 21, 2009 11:01 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] genconf
> 
> Payman Pirzadeh wrote:
>> Yes and no!
>> Sometimes there is an overlap, but sometimes I could find nothing! In the
>> simplest case, how can we avoid overlaps in a way that the crystal
> structure
>> is maintained under pbc?
>> Can the option "-dist" help here?
> 
> Replicating a box that was not designed for periodicity will always have 
> this problem. Whether the box is too small or two large, there will 
> either be steric clashes, or vacuums that will need filling. The general 
> solution is to equilibrate your box under PBC prior to replication. Now 
> the box size and the atomic spacings will be plausible, and the 
> replication will not of necessity introduce artifacts.
> 
> Mark
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-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] (no subject)

[Justin A. Lemkul]

Marc Charendoff wrote:
 
So sorry! You're absolutely right. Re the question on Zn 2+ I am asking 
about the ffgmx forcefield.
 
 


I don't believe the answers to your questions are in the public domain, for 
several reasons.  First, ffgmx is an old, deprecated force field that is 
somewhat of a hodge-podge of many different parameters (reference previous 
discussions on the list).  For any new simulation, I would strongly recommend a 
more modern force field.  Second, the official reference for the Gromos87 force 
field (the backbone of ffgmx) is the Gromos87 user's manual, which one has to 
pay a license fee to obtain.


Based on literature of more recent Gromos96 force field parameter sets (53a5 and 
53a6), I would think that coordination geometry was not involved.  Other details 
are still sparing regarding ion parameterization, aside from a small section 
describing repulsive terms between ions in the Gromos96 53a5/53a6 paper.


-Justin

 
Marc Charendoff wrote:

 > Hello,
 >
 >I am curious - is there anyway to see what assumptions were 
made when parameterizing the Zn 2+ ion? Was it tetrahedrally or 
octahedrally coordinated? With waters only or with imidazoles? Do the 
different force fields make different assumptions?  Guidance appreciated.


Without even knowing the force field to which you were referring, we
can't say anything other than to refer you to the primary literature for
that force field.

Mark





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Wrong pressure with "mdrun -rerun" option

[LuLanyuan]

Hello all,
>From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be 
>correct. However, I did a test for a box of tip3p water and found the pressure 
>results from rerun were different compared to the original results. For the 
>first MD simulation , I simulated it for 200 ps and use the neighbor list 
>update frequency 1. I used "g_energy" to extract pressure results and the 
>results were 545.384 and 1153.55 bars for the MD and rerun, respectively. The 
>gromacs version is 4.0.5.
Can anyone give me any clue?
Thanks.
Lanyuan Lu

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[gmx-users] (no subject)

[Marc Charendoff]

So sorry! You're absolutely right. Re the question on Zn 2+ I am asking about 
the ffgmx forcefield. 



Marc Charendoff wrote:
> Hello,
> 
>        I am curious - is there anyway to see what assumptions were made when 
>parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally 
>coordinated? With waters only or with imidazoles? Do the different force 
>fields make different assumptions?  Guidance appreciated.

Without even knowing the force field to which you were referring, we 
can't say anything other than to refer you to the primary literature for 
that force field.

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Re: [gmx-users] using two different combination rules for the LJ potentia

[Mark Abraham]

Ana West wrote:
Thank you so much for the kind reply. I made a mistake in my previous 
posting - I am dealing with combination rule 1 and the combination rule 
2. Initially I converted the parameters according to section 5.3.3 of 
the manual and when I did some tests to verify my force-field, the 
minimum of the potential well seemed fine but the repulsive part of the 
potential was not steep enough. The conversion did not seem to work for me.


Why is this problem of mixing combination rules even arising?

Is there sort of a qualitative way of knowing when the conversion from 
section 5.3.3 fails? (like maybe it fails when one has relatively high 
partial charges ?!?1). If I would know that then maybe I will get more 
lucky with the conversions for the other molecule and keep the 
combination rules for the one for which I know the conversion parameters 
fail.


The charges are irrelevant - these parameters are modelling vdW 
interactions.


Mark
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[gmx-users] using two different combination rules for the LJ potentia

[Ana West]

Thank you so much for the kind reply. I made a mistake in my previous  
posting - I am dealing with combination rule 1 and the combination  
rule 2. Initially I converted the parameters according to section  
5.3.3 of the manual and when I did some tests to verify my  
force-field, the minimum of the potential well seemed fine but the  
repulsive part of the potential was not steep enough. The conversion  
did not seem to work for me.


Is there sort of a qualitative way of knowing when the conversion from  
section 5.3.3 fails? (like maybe it fails when one has relatively high  
partial charges ?!?1). If I would know that then maybe I will get more  
lucky with the conversions for the other molecule and keep the  
combination rules for the one for which I know the conversion  
parameters fail.


Thank you so much! Your reply helped me.

Ana

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Re: [gmx-users] pull.ppa doesn't work

[Justin A. Lemkul]

accomp lin wrote:


hi everyone,

I;m using umbrella sampling to calculate PMF

My system is DPPC + water + protein
In pull.ppa, I set runtype = umbrella ，reftype = com_t0，
K1   = 5000  ，Pos1  = 0.0 0.0 6.0

However this came out when I finally type mdrun :
 


Reading parameter file pull.ppa
' for variable verbose, using 'no'
Next time use one of : 'no' 'yes'
' for variable runtype, using 'afm'
Next time use one of : 'afm' 'constraint' 'umbrella'
' for variable reftype, using 'com'
Next time use one of ; 'com' 'com_t0' 'dynamic' 'dynamic_t0'
.
.
.
 


Then something is badly formatted in the file.  Perhaps it was edited on a 
Windows machine and has hidden formatting characters?



——
program mdrun, VERSION 3.3.3
source code file: pullinit.c, line: 215

Fatal error:
in the index fileGN
——

It seems that mdrun doesn't recognize what I set in pull.ppa
And I don't know what's wrong with my index file, it looks all right to me.
So, can any body tell me what is going on?


Could also be related to the same formatting issues you're seeing with your .ppa 
file.


-Justin

 
Thanks!




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Re: Some questions on Tabulated Dihedral Potential

[Ran Friedman]

Hi Johannes,

Thanks for the correction - you're right of course (when deltaX = 1 it's
the same).

To be closer to the gromacs code it's
der = (y[N+1] - y[N-1]) * 0.5 * tabscale

where
tabscale = number of points per nm (or degree for angles/dihedrals).

Ran.

Johannes Kamp wrote:
> Hi Ran,
>
> are you sure the derivative is calculated as:
> der = (y[N+1] - y[N-1]) * 0.5 * deltaX
>
> and not as:
> der = (y[N+1] - y[N-1]) * 0.5 / deltaX ?
>
> The last calculation makes a little more sense to me...
>
> -Johannes
>
>
>>> Ran Friedman wrote:
 Hi,

 The numerical derivative for the Nth value y[N] is calculated as:
 der = y[N+1] - y[N-1] * 0.5 * deltaX
>>> Correction:
>>> der = (y[N+1] - y[N-1]) * 0.5 * deltaX
 where y is the potential deltaX is the difference between two
 successive values in your input (e.g., 1 if you have a table that
 goes from -180 to 180 with 361 values).

 I don't think you can print the number without changing the code,
 but it's not difficult to calculate. You can plot your forces and
 -der and see where they deviate.

 Ran.
> 
>
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[gmx-users] Re: Some questions on Tabulated Dihedral Potential

[Johannes Kamp]

Hi Ran,

are you sure the derivative is calculated as:
der = (y[N+1] - y[N-1]) * 0.5 * deltaX

and not as:
der = (y[N+1] - y[N-1]) * 0.5 / deltaX ?

The last calculation makes a little more sense to me...

-Johannes



  



Ran
Friedman wrote:
 Hi,
  
The numerical derivative for the Nth value y[N] is calculated as:
der = y[N+1] - y[N-1] * 0.5 * deltaX

Correction:
der = (y[N+1] - y[N-1]) * 0.5 * deltaX
where y
is the potential deltaX is the difference between two
successive values in your input (e.g., 1 if you have a table that goes
from -180 to 180 with 361 values).
  
I don't think you can print the number without changing the code, but
it's not difficult to calculate. You can plot your forces and -der and
see where they deviate. 
  
Ran.





  



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Re: [gmx-users] Periodic Boundary Condition Issues

[Omer Markovitch]

Try combining indices with that, use "make_ndx -h". --Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul  wrote:

> The trjconv -pbc options were designed to fix this sort of issue.
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RE: [gmx-users] invalid angle type 0

[Kukol, Andreas]

Bing Bing,

There is a topology available for POPC with ffG53a6 in the user contribution 
section.

Published in: Kukol, A., 2009. Lipid models for united-atom molecular dynamics 
simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626.

However, it currently doesn't work with Gromacs 4, but I will upload the 
working topologies as soon as the new web-site allows me to do so. In the 
meantime you may contact me off-list.

Best regards
Andreas

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Mark Abraham
> Sent: 23 July 2009 09:08
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] invalid angle type 0
>
> Bing Bing wrote:
> > Dear all,
> > I 've prepared POPC  and protein with ffG53a6 forcefield. I've  also built
> > the ligand in the protein with ffG53a6, but it is not working. Many atom
> > types in the ligand which i work on is not found in ffG53a6*.itp but if i
> > change the forcefield to ffgmx, it work fine.
> > I have tried to add-in those unrecognize atomtype into the ffG53a6bon.itp
> > and ffG53a5nb.itp from ffgmx*.itp.
>
> Don't mix force fields. See
> http://oldwiki.gromacs.org/index.php/Category:Force_Fields
>
> > The atomtype error is solved  But another
> > error again (invalid angle type 0). I'm not sure went wrong. I've check
> the
> > angle types in the ffG53a6, i couldn't see what cause this. Please advice.
> > May i know is it possible to use 2 differents forcefield in 1 system since
> > the ligand work well with ffgmx and ffG53a6 is good for lipid?
>
> No. You need to develop a topology for both parts based on the same
> force field.
>
> Mark
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Re: [gmx-users] invalid angle type 0

[Mark Abraham]

Bing Bing wrote:

Dear all,
I 've prepared POPC  and protein with ffG53a6 forcefield. I've  also built
the ligand in the protein with ffG53a6, but it is not working. Many atom
types in the ligand which i work on is not found in ffG53a6*.itp but if i
change the forcefield to ffgmx, it work fine.
I have tried to add-in those unrecognize atomtype into the ffG53a6bon.itp
and ffG53a5nb.itp from ffgmx*.itp.


Don't mix force fields. See 
http://oldwiki.gromacs.org/index.php/Category:Force_Fields



The atomtype error is solved  But another
error again (invalid angle type 0). I'm not sure went wrong. I've check the
angle types in the ffG53a6, i couldn't see what cause this. Please advice.
May i know is it possible to use 2 differents forcefield in 1 system since
the ligand work well with ffgmx and ffG53a6 is good for lipid?


No. You need to develop a topology for both parts based on the same 
force field.


Mark
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[gmx-users] invalid angle type 0

[Bing Bing]

Dear all,
I 've prepared POPC  and protein with ffG53a6 forcefield. I've  also built
the ligand in the protein with ffG53a6, but it is not working. Many atom
types in the ligand which i work on is not found in ffG53a6*.itp but if i
change the forcefield to ffgmx, it work fine.
I have tried to add-in those unrecognize atomtype into the ffG53a6bon.itp
and ffG53a5nb.itp from ffgmx*.itp.The atomtype error is solved  But another
error again (invalid angle type 0). I'm not sure went wrong. I've check the
angle types in the ffG53a6, i couldn't see what cause this. Please advice.
May i know is it possible to use 2 differents forcefield in 1 system since
the ligand work well with ffgmx and ffG53a6 is good for lipid?

regards,
bing
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