Thanks.
I add igb=1 in the input file, but I get another problem. Since in my intial mdcrd files, they have the counter ions and water molecules, now I remove the ions and water molecules and get the new mdcrd trajactory file by Ptraj in order to get SASA. When I run the Sander, it shows "bad atom type" that are corresponding to the counter ions. But If I didn't use prmtop, it shows: Unit 8 Error on OPEN: prmtop ( I think prmtop probably should not be ignored).
What I should do now? I really want to solve this problem to get the SASA.
Thanks
Carlos Simmerling <carlos.simmerling.gmail.com> wrote: it won't matter, igb=1 is fine. it only matters if you want to use the GB energies.
On 3/1/07, Esther Brugger < esther_brugger.yahoo.com> wrote:Thanks!
I remove the water by using ptraj, and doing the calcuation as following:
$AMBERHOME/exe/sander -O -i 1_SASA.in -c 1_initial.rst -p 1_wat.prmtop -x 1_SASA.mdcrd -o LV_SASA.out
After runing it, it shows:
GB/SA calculation is performed only when igb>0
I really don't know which option I should select in igb. Could you please give me some suggestions?
Thanks a lot!
Carlos Simmerling < carlos.simmerling.gmail.com> wrote: use ptraj to remove the water with the strip command. you can't calculate SASA with water there.
also the -c is not right for the mdcrd file. check the amber manual for details.
On 3/1/07, Esther Brugger < esther_brugger.yahoo.com> wrote: Thanks for your reply. Here is the command and input file that I used.
Acturally, this mdcrd trajactory file has the water in it, I want to remove the water to calculate the SASA, but I really don't know how to do it. Thanks again for your help!
$AMBERHOME/exe/sander -O -i SASA.in -p prmtop -c mdcrd -o SASA.out
&cntrl
imin = 5,
gbsa=2,
surften=1
/
Carlos Simmerling < carlos.simmerling.gmail.com> wrote: can you tell us what you did? send the sander run script and input.
On 2/28/07, Esther Brugger < esther_brugger.yahoo.com > wrote:Dear Carlos,
Thanks a lot for your reply.
I tried as you said, it has some prolems when it runs. it shows:
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
sander 081A86F6 Unknown Unknown Unknown
.....
I don't know why......Do you have any suggestion for that?
Thanks,
Carlos Simmerling < carlos.simmerling.gmail.com> wrote: you might try using the gbsa optino, especially gbsa=2 and surften=1. this
way the SASA energy will actually be the SASA. You can use imin=5 to read the
trajectory and report SASA for each frame.
On 2/28/07, Esther Brugger <esther_brugger.yahoo.com> wrote: Dear Everyone,
I am trying to calculate the "solvent accessible surface area (SASA)" of a molecule through a trajectory file obtained by MD simulation (AMBER8). I removed the water molecules (TIP3P model) and counter ions from the systym by using Ptraj. I have some problems to do the calculation of SASA.
(1) I checked the archive file for the discussion, it seems "molsurf" program can calculate SASA if I put the proble radius at zero, is it correct? But it need pqrfile, I really don't know how I can get this file. And is it possible to calculate SASA by mdcrd trajectory file in molsurf?
(2) Someone suggested to use the software (SURFace) in Honig Lab, but I found it needs the pdb file for the calculations. Is there someone know how to convert the trajactory (mdcrd) file to pdb file for each of the frame?
(3) I also found somebody suggested to usd the software "naccess", but I met some problems to decrypt the file, because I didn't find the commands "crypt/des/mcrypt" in my Linux system. Dose someone could give me some suggestions about that?
Sorry, I post a lot of questions, I really wish someone could help me to solve these problelms,
Thanks for your any help!
Esther B.
---------------------------------
Bored stiff? Loosen up...
Download and play hundreds of games for free on Yahoo! Games.
Carlos Simmerling < carlos.simmerling.gmail.com > wrote: can you tell us what you did? send the sander run script and input.
On 2/28/07, Esther Brugger <esther_brugger.yahoo.com > wrote: Dear Carlos,
Thanks a lot for your reply.
I tried as you said, it has some prolems when it runs. it shows:
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
sander 081A86F6 Unknown Unknown Unknown
.....
I don't know why......Do you have any suggestion for that?
Thanks,
Carlos Simmerling < carlos.simmerling.gmail.com> wrote: you might try using the gbsa optino, especially gbsa=2 and surften=1. this
way the SASA energy will actually be the SASA. You can use imin=5 to read the
trajectory and report SASA for each frame.
On 2/28/07, Esther Brugger <esther_brugger.yahoo.com> wrote: Dear Everyone,
I am trying to calculate the "solvent accessible surface area (SASA)" of a molecule through a trajectory file obtained by MD simulation (AMBER8). I removed the water molecules (TIP3P model) and counter ions from the systym by using Ptraj. I have some problems to do the calculation of SASA.
(1) I checked the archive file for the discussion, it seems "molsurf" program can calculate SASA if I put the proble radius at zero, is it correct? But it need pqrfile, I really don't know how I can get this file. And is it possible to calculate SASA by mdcrd trajectory file in molsurf?
(2) Someone suggested to use the software (SURFace) in Honig Lab, but I found it needs the pdb file for the calculations. Is there someone know how to convert the trajactory (mdcrd) file to pdb file for each of the frame?
(3) I also found somebody suggested to usd the software "naccess", but I met some problems to decrypt the file, because I didn't find the commands "crypt/des/mcrypt" in my Linux system. Dose someone could give me some suggestions about that?
Sorry, I post a lot of questions, I really wish someone could help me to solve these problelms,
Thanks for your any help!
Esther B.
---------------------------------
Bored stiff? Loosen up...
Download and play hundreds of games for free on Yahoo! Games.
Esther B.
---------------------------------
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Esther B.
---------------------------------
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115
===================================================================
Esther B.
---------------------------------
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Received on Sun Mar 04 2007 - 06:07:46 PST
