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
>
> ==**==
> --
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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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