Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Justin Lemkul 



On 11/26/12 9:43 AM, Venkat Reddy wrote:

Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?




I have no idea.  I haven't used PRODRG in a very long time.

-Justin


On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul  wrote:




On 11/26/12 9:35 AM, Venkat Reddy wrote:


Dear Justin,

One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?




PRODRG doesn't even do a very good job of being compatible with 43A1, so
if you re-derive the charges correctly, the result is compatible with 53A6.
  PRODRG basically just uses 43A1 atom types, the names of which are largely
the same in 53A6, even if the parameters are slightly different, and thus I
view PRODRG as a method to create generic Gromos96 topologies, given that
the user has to do a fair amount of work to create a usable topology anyway.

-Justin

  On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul  wrote:





On 11/26/12 9:12 AM, Venkat Reddy wrote:

  Dear Justin,

I haven't touched the *Mass column.* I have edited the charges only
using
"gedit" in linux.


  Regardless, the masses I pointed out are wrong.  You should still do

the
test to #include the original topology and see if it works, then if it
does, figure out the source of the error in your file.

-Justin


  On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:





On 11/26/12 12:58 AM, Venkat Reddy wrote:

   Dear all,


I am simulating a Protein-Drug complex. I am following Justin's
tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me
the
ESP
charges. I have edited the charges in the itp file using the
*Gaussian*'s
ESP charges*. *Then I am getting this strange error.

 *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*


   Probably there are some hidden line ending problems.  Did you edit
the


file with a plain text editor?

Also note...

 24   CH2 1  ORP  C5 40.354  13.0190

 *25   CH1 1  ORP  C4 4   -0.024  14.0270*



  These masses don't make sense.  CH2 should have a mass of 14.027 and

CH1
should have a mass of 13.019.  I've never seen PRODRG get something
like
this wrong; were you sure to carefully change the file?  It seems
something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.
  If
grompp succeeds using the PRODRG topology (stop using it after that
point),
then the error arose due to something you did when editing the file.

-Justin

--
==**==



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**<
http://vt.edu/Pages/Personal/**justin



http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justin








==**==


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====

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>




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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Venkat Reddy 
Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?


On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul  wrote:

>
>
> On 11/26/12 9:35 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>>
>> One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
>> topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
>> mix 53A6 and 43A1?
>>
>>
>>
> PRODRG doesn't even do a very good job of being compatible with 43A1, so
> if you re-derive the charges correctly, the result is compatible with 53A6.
>  PRODRG basically just uses 43A1 atom types, the names of which are largely
> the same in 53A6, even if the parameters are slightly different, and thus I
> view PRODRG as a method to create generic Gromos96 topologies, given that
> the user has to do a fair amount of work to create a usable topology anyway.
>
> -Justin
>
>  On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>>>
>>>  Dear Justin,
 I haven't touched the *Mass column.* I have edited the charges only
 using
 "gedit" in linux.


  Regardless, the masses I pointed out are wrong.  You should still do
>>> the
>>> test to #include the original topology and see if it works, then if it
>>> does, figure out the source of the error in your file.
>>>
>>> -Justin
>>>
>>>
>>>  On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:



> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>
>   Dear all,
>
>> I am simulating a Protein-Drug complex. I am following Justin's
>> tutorial.
>> I
>> have used *PRODRG *for generating topology. *Gaussian *has given me
>> the
>> ESP
>> charges. I have edited the charges in the itp file using the
>> *Gaussian*'s
>> ESP charges*. *Then I am getting this strange error.
>>
>> *ERROR 1 [file protein.top, line 75]:*
>> *  atom C4 (Res ORP-1) has mass 0*
>> *
>> *
>> *
>> *
>> *
>> *
>> *ERROR 2 [file protein.top, line 75]:*
>> *  atom C14 (Res ORP-1) has mass 0*
>>
>>
>>   Probably there are some hidden line ending problems.  Did you edit
>> the
>>
> file with a plain text editor?
>
> Also note...
>
> 24   CH2 1  ORP  C5 40.354  13.0190
>
> *25   CH1 1  ORP  C4 4   -0.024  14.0270*
>>
>>
>>  These masses don't make sense.  CH2 should have a mass of 14.027 and
> CH1
> should have a mass of 13.019.  I've never seen PRODRG get something
> like
> this wrong; were you sure to carefully change the file?  It seems
> something
> has gone very wrong here.
>
> Compare the original topology (from PRODRG) with the one you edited.
>  If
> grompp succeeds using the PRODRG topology (stop using it after that
> point),
> then the error arose due to something you did when editing the file.
>
> -Justin
>
> --
> ==**==
>
>
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**<
> http://vt.edu/Pages/Personal/**justin
> >
>  http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justin
> >
>
>>
>>
> ==**==
>
>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> >
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>>  * Please search the archive at http://www.gromacs.org/**
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>
> Mailing_Lists/Search Mailing_Lists/Search
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>

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Justin Lemkul 



On 11/26/12 9:35 AM, Venkat Reddy wrote:

Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?




PRODRG doesn't even do a very good job of being compatible with 43A1, so if you 
re-derive the charges correctly, the result is compatible with 53A6.  PRODRG 
basically just uses 43A1 atom types, the names of which are largely the same in 
53A6, even if the parameters are slightly different, and thus I view PRODRG as a 
method to create generic Gromos96 topologies, given that the user has to do a 
fair amount of work to create a usable topology anyway.


-Justin


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul  wrote:




On 11/26/12 9:12 AM, Venkat Reddy wrote:


Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.



Regardless, the masses I pointed out are wrong.  You should still do the
test to #include the original topology and see if it works, then if it
does, figure out the source of the error in your file.

-Justin



On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:




On 11/26/12 12:58 AM, Venkat Reddy wrote:

  Dear all,

I am simulating a Protein-Drug complex. I am following Justin's
tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me the
ESP
charges. I have edited the charges in the itp file using the
*Gaussian*'s
ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the

file with a plain text editor?

Also note...

24   CH2 1  ORP  C5 40.354  13.0190


   *25   CH1 1  ORP  C4 4   -0.024  14.0270*



These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
should have a mass of 13.019.  I've never seen PRODRG get something like
this wrong; were you sure to carefully change the file?  It seems
something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.  If
grompp succeeds using the PRODRG topology (stop using it after that
point),
then the error arose due to something you did when editing the file.

-Justin

--
====


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>




====

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--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
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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Justin A. Lemkul, Ph.D.
Research Scientist
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] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Venkat Reddy 
Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul  wrote:

>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> I haven't touched the *Mass column.* I have edited the charges only using
>> "gedit" in linux.
>>
>>
> Regardless, the masses I pointed out are wrong.  You should still do the
> test to #include the original topology and see if it works, then if it
> does, figure out the source of the error in your file.
>
> -Justin
>
>
>> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>>>
>>>  Dear all,
 I am simulating a Protein-Drug complex. I am following Justin's
 tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me the
 ESP
 charges. I have edited the charges in the itp file using the
 *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the
>>> file with a plain text editor?
>>>
>>> Also note...
>>>
>>>24   CH2 1  ORP  C5 40.354  13.0190
>>>
   *25   CH1 1  ORP  C4 4   -0.024  14.0270*


>>> These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
>>> should have a mass of 13.019.  I've never seen PRODRG get something like
>>> this wrong; were you sure to carefully change the file?  It seems
>>> something
>>> has gone very wrong here.
>>>
>>> Compare the original topology (from PRODRG) with the one you edited.  If
>>> grompp succeeds using the PRODRG topology (stop using it after that
>>> point),
>>> then the error arose due to something you did when editing the file.
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> >
>>>
>>>
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Venkat Reddy 
Thanks Justin...I will certainly do.


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul  wrote:

>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> I haven't touched the *Mass column.* I have edited the charges only using
>> "gedit" in linux.
>>
>>
> Regardless, the masses I pointed out are wrong.  You should still do the
> test to #include the original topology and see if it works, then if it
> does, figure out the source of the error in your file.
>
> -Justin
>
>
>> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>>>
>>>  Dear all,
 I am simulating a Protein-Drug complex. I am following Justin's
 tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me the
 ESP
 charges. I have edited the charges in the itp file using the
 *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the
>>> file with a plain text editor?
>>>
>>> Also note...
>>>
>>>24   CH2 1  ORP  C5 40.354  13.0190
>>>
   *25   CH1 1  ORP  C4 4   -0.024  14.0270*


>>> These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
>>> should have a mass of 13.019.  I've never seen PRODRG get something like
>>> this wrong; were you sure to carefully change the file?  It seems
>>> something
>>> has gone very wrong here.
>>>
>>> Compare the original topology (from PRODRG) with the one you edited.  If
>>> grompp succeeds using the PRODRG topology (stop using it after that
>>> point),
>>> then the error arose due to something you did when editing the file.
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> >
>>>
>>>
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Justin Lemkul 



On 11/26/12 9:12 AM, Venkat Reddy wrote:

Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.



Regardless, the masses I pointed out are wrong.  You should still do the test to 
#include the original topology and see if it works, then if it does, figure out 
the source of the error in your file.


-Justin



On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:




On 11/26/12 12:58 AM, Venkat Reddy wrote:


Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me the
ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

   *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*



Probably there are some hidden line ending problems.  Did you edit the
file with a plain text editor?

Also note...

   24   CH2 1  ORP  C5 40.354  13.0190

  *25   CH1 1  ORP  C4 4   -0.024  14.0270*



These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
should have a mass of 13.019.  I've never seen PRODRG get something like
this wrong; were you sure to carefully change the file?  It seems something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.  If
grompp succeeds using the PRODRG topology (stop using it after that point),
then the error arose due to something you did when editing the file.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
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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Justin A. Lemkul, Ph.D.
Research Scientist
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] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Venkat Reddy 
Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.


On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul  wrote:

>
>
> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>
>> Dear all,
>> I am simulating a Protein-Drug complex. I am following Justin's tutorial.
>> I
>> have used *PRODRG *for generating topology. *Gaussian *has given me the
>> ESP
>> charges. I have edited the charges in the itp file using the *Gaussian*'s
>> ESP charges*. *Then I am getting this strange error.
>>
>>   *ERROR 1 [file protein.top, line 75]:*
>> *  atom C4 (Res ORP-1) has mass 0*
>> *
>> *
>> *
>> *
>> *
>> *
>> *ERROR 2 [file protein.top, line 75]:*
>> *  atom C14 (Res ORP-1) has mass 0*
>>
>>
> Probably there are some hidden line ending problems.  Did you edit the
> file with a plain text editor?
>
> Also note...
>
>   24   CH2 1  ORP  C5 40.354  13.0190
>>  *25   CH1 1  ORP  C4 4   -0.024  14.0270*
>>
>
> These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
> should have a mass of 13.019.  I've never seen PRODRG get something like
> this wrong; were you sure to carefully change the file?  It seems something
> has gone very wrong here.
>
> Compare the original topology (from PRODRG) with the one you edited.  If
> grompp succeeds using the PRODRG topology (stop using it after that point),
> then the error arose due to something you did when editing the file.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>  posting!
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

2012-11-26 Thread Justin Lemkul 



On 11/26/12 12:58 AM, Venkat Reddy wrote:

Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial. I
have used *PRODRG *for generating topology. *Gaussian *has given me the ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

  *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*



Probably there are some hidden line ending problems.  Did you edit the file with 
a plain text editor?


Also note...


 24   CH2 1  ORP  C5 40.354  13.0190
 *25   CH1 1  ORP  C4 4   -0.024  14.0270*


These masses don't make sense.  CH2 should have a mass of 14.027 and CH1 should 
have a mass of 13.019.  I've never seen PRODRG get something like this wrong; 
were you sure to carefully change the file?  It seems something has gone very 
wrong here.


Compare the original topology (from PRODRG) with the one you edited.  If grompp 
succeeds using the PRODRG topology (stop using it after that point), then the 
error arose due to something you did when editing the file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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 1: atom C4 (Res ORP-1) has mass 0

2012-11-25 Thread Venkat Reddy 
Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial. I
have used *PRODRG *for generating topology. *Gaussian *has given me the ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

 *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*

But itp file has corresponding masses for both *C14 *and *C4.*
*
*
My itp file is
*
*
[ moleculetype ]
; Name nrexcl
ORP  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1 F 1  ORP  F4 1   -0.203  18.9984
 2  CCl4 1  ORP C23 10.727  12.0110
 3 F 1  ORP  F5 1   -0.213  18.9984
 4 F 1  ORP  F6 2   -0.230  18.9984
 5 C 1  ORP C21 2   -0.123  12.0110
 6   CR1 1  ORP C22 2   -0.096  12.0110
 7HC 1  ORP H9Q 20.100   1.0080
 8   CR1 1  ORP C20 2   -0.049  12.0110
 9HC 1  ORP H20 20.061   1.0080
10 C 1  ORP C19 2   -0.112  12.0110
11  CCl4 1  ORP C24 20.746  12.0110
12 F 1  ORP  F8 2   -0.220  18.9984
13 F 1  ORP  F9 3   -0.221  18.9984
14 F 1  ORP  F7 3   -0.226  18.9984
15   CR1 1  ORP C18 3   -0.153  12.0110
16HC 1  ORP H18 30.079   1.0080
17 C 1  ORP C17 30.161  12.0110
18   CH2 1  ORP C16 30.086  14.0270
19 N 1  ORP  N2 3   -0.612  14.0067
20 C 1  ORP C25 30.846  12.0110
21 O 1  ORP  O3 4   -0.449  15.9994
22OA 1  ORP  O4 4   -0.299  15.9994
23   CH3 1  ORP C26 40.142  15.0350
24   CH2 1  ORP  C5 40.354  13.0190
*25   CH1 1  ORP  C4 4   -0.024  14.0270*
26   CH2 1  ORP  C3 40.268  13.0190
27   CH2 1  ORP  C2 40.066  14.0270
28   CH3 1  ORP  C1 5   -0.073  15.0350
29 C 1  ORP  C6 5   -0.194  12.0110
30   CR1 1  ORP  C7 60.075  12.0110
31HC 1  ORP  H7 60.005   1.0080
32 C 1  ORP  C8 6   -0.168  12.0110
33  CCl4 1  ORP C15 60.711  12.0110
34 F 1  ORP  F2 6   -0.214  18.9984
35 F 1  ORP  F3 6   -0.208  18.9984
36 F 1  ORP  F1 6   -0.215  18.9984
37   CR1 1  ORP  C9 7   -0.030  12.0110
38HC 1  ORP  H9 70.066   1.0080
39   CR1 1  ORP C10 7   -0.146  12.0110
40HC 1  ORP H10 70.094   1.0080
41 C 1  ORP C11 70.340  12.0110
42NR 1  ORP  N1 7   -0.647  14.0067
43 C 1  ORP C12 70.843  12.0110
44 O 1  ORP  O1 7   -0.409  15.9994
45OA 1  ORP  O2 8   -0.466  15.9994
46   CH2 1  ORP C13 80.292  14.0270
*47   CH3 1  ORP C14 9   -0.064  15.0350*

Thanks for your valuable time
-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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