AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA problems in AMBER9

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Mon Oct 06 2008 - 08:04:37 CDT

Adding the following line to $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm:
  print OUT " fillratio=3 \n"; should solve the problem according to

http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html

HTH

--alessandro

2008/10/6 Ray Luo <rluo_at_uci.edu>:
> The error message says that you should change fillratio NOT scale to a
> larger number ...
>
> All the best,
> Ray
>
> 2008/10/5 欧阳德方 <ouyangdf1978_at_hotmail.com>:
>>
>> Hi, all,
>>
>> When I calculate the binding energy of RNA-small molecule interaction by MM_PBSA in AMBER9. Input file is as following:
>>
>> PREFIX snapshot
>> PATH ./
>> #
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> #
>> COMPT ./den4_complex_major_vac.prmtop
>> RECPT ./rna_vac.prmtop
>> LIGPT ./dendrimer4.prmtop
>> #
>> GC 0
>> AS 0
>> DC 0
>> #
>> MM 1
>> GB 1
>> PB 1
>> MS 1
>> #
>> NM 0
>> #
>> PROC 2
>> REFE 0
>> INDI 1.0
>> EXDI 80.0
>> SCALE 2
>> LINIT 1000
>> PRBRAD 1.4
>> ISTRNG 0.0
>> RADIOPT 0
>> NPOPT 1
>> CAVITY_SURFTEN 0.0072
>> CAVITY_OFFSET 0.00
>> #
>> SURFTEN 0.0072
>> SURFOFF 0.00
>> #
>> DIELC 1.0
>> #
>> #
>> IGB 2
>> GBSA 1
>> SALTCON 0.00
>> EXTDIEL 80.0
>> INTDIEL 1.0
>> #
>> SURFTEN 0.0072
>> SURFOFF 0.00
>> #
>> #
>> PROBE 0.0
>> #
>>
>> But it shows "---snapshot_lig.crd.17 not successful---"
>> The output file shows
>> "---PB Bomb in setgrd (): focusing grid too large 2
>> reset fillratio to a large number 2.000"
>>
>> According previous post, I change SCALE 2.0 to 4.0 (or 3.0). But new problems appears.
>> The output file shows:
>> "---
>> WARNING: Missing PB for PB in 0 -> Taken from -1
>> WARNING: Missing PB for PB in 1 -> Taken from 0
>> WARNING: Missing PB for PB in 2 -> Taken from 1
>> ---
>> =>> Calc delta from raw data"
>>
>> Also the command lines shows:
>> " ---
>> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
>> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
>> No data for 0+2 PB PB 0"
>>
>> I cannot get the final statistical output file.
>>
>> Could u tell me the reasons and how to solve it?
>>
>> Thanks for your help,
>>
>> Ouyang
>>
>> School of Pharmacy
>> The University of Queensland
>> Brisbane, Australia
>>
>>
>>
>>
>>
>> _________________________________________________________________
>> 新版手机MSN，满足你多彩需求！参加抢鲜体验活动，领取特色奖品！
>> http://mobile.msn.com.cn/
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
[ ]s

--alessandro
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu